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BMRB: 34290

6GVT

Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules

Authors

Boudet, J., Wiegand, T., Meier, B.H., Lipps, G., Allain, F.H.-T.

Assembly

functional pRN1 primase/DNA Complex

Entity

1. functional pRN1 primase/DNA Complex, entity 1 (polymer, Thiol state: not present), 9 monomers, 2769.757 Da Detail

CTGTGCTCA

2. functional pRN1 primase/DNA Complex, entity 2 (polymer, Thiol state: all disulfide bound), 115 monomers, 13503.53 Da Detail

TVVEFEELRK ELVKRDSGKP VEKIKEEICT KSPPKLIKEI ICENKTYADV NIDRSRGDWH VILYLMKHGV TDPDKILELL PRDSKAKENE KWNTQKYFVI TLSKAWSVVK KYLEA

3. functional pRN1 primase/DNA Complex, entity ATP (non-polymer), 507.181 × 2 Da
4. functional pRN1 primase/DNA Complex, entity MG (non-polymer), 24.305 × 2 Da

Total weight

17336.258 Da

Max. entity weight

13503.53 Da

Entity Connection

disulfide 1, metal coordination 8 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	2:CYS29:SG	2:CYS42:SG
2	metal coordination	sing	2:ASP53:OD2	4:MG1:MG
3	metal coordination	sing	2:GLU88:OE2	4:MG1:MG
4	metal coordination	sing	3:ATP1:O2G	4:MG1:MG
5	metal coordination	sing	3:ATP1:O2B	4:MG1:MG
6	metal coordination	sing	3:ATP1:O1A	4:MG1:MG
7	metal coordination	sing	3:ATP1:O1G	4:MG1:MG
8	metal coordination	sing	3:ATP1:O1B	4:MG1:MG
9	metal coordination	sing	3:ATP1:O1A	4:MG1:MG

Source organism

Sulfolobus islandicus

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 78.4 %, Completeness (bb): 76.7 % Detail

Polymer type: polydeoxyribonucleotide polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.4 % (1196 of 1525)	83.7 % (709 of 847)	68.0 % (381 of 560)	89.8 % (106 of 118)
Backbone	76.7 % (570 of 743)	90.7 % (264 of 291)	60.5 % (207 of 342)	90.0 % (99 of 110)
Sidechain	81.3 % (727 of 894)	80.0 % (445 of 556)	83.3 % (275 of 330)	87.5 % (7 of 8)
Aromatic	74.6 % (85 of 114)	74.2 % (49 of 66)	73.3 % (33 of 45)	100.0 % (3 of 3)
Methyl	92.8 % (129 of 139)	94.4 % (67 of 71)	91.2 % (62 of 68)

1. entity 1

CTGTGCTCA

2. entity 2

TVVEFEELRK ELVKRDSGKP VEKIKEEICT KSPPKLIKEI ICENKTYADV NIDRSRGDWH VILYLMKHGV TDPDKILELL PRDSKAKENE KWNTQKYFVI TLSKAWSVVK KYLEA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 100% D2O

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM [U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 15N]	1.0 mM
10	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
11	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
12	magnesium	natural abundance	10.0 mM

Sample #4

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
14	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
15	magnesium	natural abundance	10.0 mM
16	pRN1 the helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM

Sample #5

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

Sample #6

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	pRN1 helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM
22	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
23	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
24	magnesium	natural abundance	10.0 mM

Sample #7

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium, 100% D2O

#	Name	Isotope labeling	Concentration
25	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	1.0 mM
26	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
27	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
28	magnesium	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	1.0
¹H	water	protons	4.7 ppm	internal	direct	0.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.0

Referencing offset: 0.18 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	1.0
¹H	water	protons	4.7 ppm	internal	direct	0.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.0

Referencing offset: 0.18 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.7 ppm	internal	direct	1.0
¹H	water	protons	4.7 ppm	internal	direct	0.0
¹⁵N	water	protons	4.7 ppm	internal	direct	0.0

Referencing offset: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6GVQ, Strand ID: B Detail

Release date

2018-09-25

Citation

A Small Helical Bundle Prepares Primer Synthesis by Binding Two Nucleotides that Enhance Sequence-Specific Recognition of the DNA Template
Boudet, J., Devillier, J.C., Wiegand, T., Salmon, L., Meier, B.H., Lipps, G., Allain, F.H.-T.
Cell (2018), 176, 154-166, PubMed 30595448 , DOI 10.1016/j.cell.2018.11.031 , Abstract

Related entities 2. functional pRN1 primase/DNA Complex, entity 2, : 1 : 4 entities Detail

Experiments performed 36 experiments Detail

1 3D HNCA

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

2 3D HN(CO)CA

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

3 3D HNCACB

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

5 3D HNCO

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

6 3D C(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

7 3D H(CCO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

8 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

10 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

11 3D 1H-13C NOESY aromatic

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.7 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 0.7 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 100% D2O

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

12 3D 1H-15N NOESY

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 1.0 mM [U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
9	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 15N]	1.0 mM
10	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
11	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
12	magnesium	natural abundance	10.0 mM

13 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
21	pRN1 helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM
22	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
23	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
24	magnesium	natural abundance	10.0 mM

14 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
21	pRN1 helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM
22	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
23	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
24	magnesium	natural abundance	10.0 mM

15 2D 1H-1H NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
14	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
15	magnesium	natural abundance	10.0 mM
16	pRN1 the helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM

16 2D 1H-1H TOCSY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
9	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 15N]	1.0 mM
10	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
11	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
12	magnesium	natural abundance	10.0 mM

17 2D 1H-13C HSQC aromatic

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

18 2D 1H-13C HSQC aliphatic

Instrument

Bruker AVANCE III - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

19 2D-F1fF2f-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

20 2D-F2f-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

21 3D-13C-aliphatic-HfilteredHedited-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

22 3D-13C-aliphatic-HfilteredHedited-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
5	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	0.7 mM
6	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	0.7 mM
7	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
8	magnesium	natural abundance	10.0 mM

23 3D-13C-aromatic-HfilteredHedited-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 1.0 mM [U-100% 13C] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium, 100% D2O

#	Name	Isotope labeling	Concentration
25	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	1.0 mM
26	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
27	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
28	magnesium	natural abundance	10 mM

24 3D-13C-aromatic-HfilteredHedited-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
25	pRN1 helix bundle domain in complex with DNA and ATP	[U-100% 13C]	1.0 mM
26	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
27	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
28	magnesium	natural abundance	10 mM

25 2D-imino-NOESY

Instrument

Bruker AVANCE III - 700 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 5.0, Details 1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
14	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
15	magnesium	natural abundance	10.0 mM
16	pRN1 the helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM

26 2D-natural-abundance-Chsqc

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.0 mM pRN1 the helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
14	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
15	magnesium	natural abundance	10.0 mM
16	pRN1 the helix bundle domain in complex with DNA and ATP	natural abundance	1.0 mM

27 DARR

Instrument

Bruker AVANCE III - 850 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 278 K, pH 7.0, Details 4.0 mM [U-99% 13C; U-99% 15N] functional-pRN1-primase, 4.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 10.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10.0 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

28 NCX(R)

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

29 NCX(W)

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

30 CHHP

Instrument

Bruker AVANCE III - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

31 NHHP

Instrument

Bruker AVANCE III - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

32 31P CPMAS

Instrument

Bruker AVANCE III - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

33 31P-31P-DARR

Instrument

Bruker AVANCE III - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

34 31P CPMAS

Instrument

Bruker AVANCE III - 850 MHz

Sample

#	Name	Isotope labeling	Concentration
17	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	4.0 mM
18	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	10.0 mM
19	magnesium	natural abundance	10.0 mM
20	functional-pRN1-primase	[U-99% 13C; U-99% 15N]	4.0 mM

35 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

36 2D 1H-15N HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 1.0 mM [U-99% 13C; U-99% 15N] pRN1 helix bundle domain in complex with DNA and ATP, 1.0 mM DNA (5'-D(*CP*TP*GP*TP*GP*CP*TP*CP*A)-3'), 4.0 mM ADENOSINE-5'-TRIPHOSPHATE, 10 mM magnesium, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	pRN1 helix bundle domain in complex with DNA and ATP	[U-99% 13C; U-99% 15N]	1.0 mM
2	DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3')	natural abundance	1.0 mM
3	ADENOSINE-5'-TRIPHOSPHATE	natural abundance	4.0 mM
4	magnesium	natural abundance	10 mM

NMR combined restraints 7 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34290_6gvt.nef
Input source #2: Coordindates	6gvt.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
B:284:CYS:SG	B:297:CYS:SG	oxidized, CA 58.54, CB 40.746 ppm	oxidized, CA 56.05, CB 38.932 ppm	2.033

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
2:53:ASP:OD2	4:1:MG:MG	unknown	unknown	n/a
2:88:GLU:OE2	4:2:MG:MG	unknown	unknown	n/a
3:1:ATP:O2G	4:1:MG:MG	unknown	unknown	n/a
3:1:ATP:O2B	4:1:MG:MG	unknown	unknown	n/a
3:1:ATP:O1A	4:1:MG:MG	unknown	unknown	n/a
3:2:ATP:O1G	4:2:MG:MG	unknown	unknown	n/a
3:2:ATP:O1B	4:2:MG:MG	unknown	unknown	n/a
3:2:ATP:O1A	4:2:MG:MG	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
C	1	MG	MAGNESIUM ION	Distance restraints
C	2	MG	MAGNESIUM ION	None
D	1	ATP	ADENOSINE-5'-TRIPHOSPHATE	Distance restraints
D	2	ATP	ADENOSINE-5'-TRIPHOSPHATE	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

---------
CTGTGCTCA
|||||||||
CTGTGCTCA

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--260-------270-------280-------290-------300-------310-------320-------330-------340-------350-----
TVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
TVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVI
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--360-------370
TLSKAWSVVKKYLEA
|||||||||||||||
TLSKAWSVVKKYLEA
-------110-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	9	0	0	100.0
B	B	115	0	0	100.0

Content subtype: combined_34290_6gvt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	9		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1194		100.0 (chain: A, length: 9), 93.0 (chain: B, length: 115)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	156 (1)	noe	88.9 (chain: A, length: 9), 19.1 (chain: B, length: 115), 50.0 (chain: C, length: 2), 50.0 (chain: D, length: 2)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	OK	3433 (1)	noe	100.0 (chain: A, length: 9), 93.0 (chain: B, length: 115)
3	Distance restraints	DYANA/DIANA_distance_constraints_6	Warning	34 (1)	undefined	11.1 (chain: A, length: 9), 3.5 (chain: B, length: 115), 50.0 (chain: C, length: 2), 50.0 (chain: D, length: 2)
4	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	216 (1)	hbond	67.8 (chain: B, length: 115), 50.0 (chain: C, length: 2), 50.0 (chain: D, length: 2)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	176 (176)	.	100.0 (chain: A, length: 9), 93.0 (chain: B, length: 115)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 115, Sequence coverage: 93.0%
- Total number of assignments
  - ¹H chemical shifts: 714
  - ¹³C chemical shifts: 376
  - ¹⁵N chemical shifts: 104
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 88.9%
  - Entity_assembly_ID: B, Chain length: 115, Sequence coverage: 19.1%
  - Entity_assembly_ID: C, Chain length: 2, Sequence coverage: 50.0%
  - Entity_assembly_ID: D, Chain length: 2, Sequence coverage: 50.0%
- Total number of restraints: 155
- Weight of restraints: 1.0 (155)
- Potential type of restraints: upper-bound-parabolic (155)
- Range of distance target values: 0.0, 10.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 100.0%
    - Entity_assembly_ID: B, Chain length: 115, Sequence coverage: 93.0%
  - Total number of restraints: 3432
  - Weight of restraints: 1.0 (3432)
  - Potential type of restraints: upper-bound-parabolic (3432)
  - Range of distance target values: 0.0, 6.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
    - Chain_ID: C
      None
    - Chain_ID: D
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_6
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 11.1%
      - Entity_assembly_ID: B, Chain length: 115, Sequence coverage: 3.5%
      - Entity_assembly_ID: C, Chain length: 2, Sequence coverage: 50.0%
      - Entity_assembly_ID: D, Chain length: 2, Sequence coverage: 50.0%
    - Total number of restraints: 34
    - Weight of restraints: 1.0 (34)
    - Potential type of restraints: upper-bound-parabolic (34)
    - Range of distance target values: 2.7, 50.0 (Å)
    - Histogram of distance target values
    - Histogram of discrepancy in distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
      - Chain_ID: C
      - Chain_ID: D
    - Distance restraints on contact map
    - Saveframe: DYANA/DIANA_distance_constraints_3
      - Status: Warning
      - Experiment type: hbond
      - Sequence coverage of experimental data
        Entity_assembly_ID: B, Chain length: 115, Sequence coverage: 67.8%
        --260-------270-------280-------290-------300-------310-------320-------330-------340-------350----- TVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVI ||||||||||||||| | |||||||| |||||||| ||||||||||||||| ||| ||| ||| |||||||| TVVEFEELRKELVKR.....V.KIKEEICT....KLIKEIIC...........RSRGDWHVILYLMKH....PDK.LEL........ENE..NTQKYFVI --260-------270-------280-------290-------300-------310-------320-------330-------340-------350----- --360-------370 TLSKAWSVVKKYLEA |||||||||||||| TLSKAWSVVKKYLE --360---------
        Entity_assembly_ID: C, Chain length: 2, Sequence coverage: 50.0%
        -- XX | X -
        Entity_assembly_ID: D, Chain length: 2, Sequence coverage: 50.0%
        -- XX | X -
      - Total number of restraints: 216
        Total hydrogen bond restraints: 216
        O...h-N (too close!): 51
        O...H-x (too close!): 51
        O...h-N: 51
        O...H-x: 51
        Inter-chain: 12
        O...H-x (too close!): 6
        O...H-x: 6
      - Weight of restraints: 1.0 (216)
        Total hydrogen bond restraints: 1.0 (216)
        O...h-N (too close!): 1.0 (51)
        O...H-x (too close!): 1.0 (51)
        O...h-N: 1.0 (51)
        O...H-x: 1.0 (51)
        Inter-chain: 1.0 (12)
        O...H-x (too close!): 1.0 (6)
        O...H-x: 1.0 (6)
      - Potential type of restraints: upper-bound-parabolic (216)
        Total hydrogen bond restraints: upper-bound-parabolic (216)
        O...h-N (too close!): upper-bound-parabolic (51)
        O...H-x (too close!): upper-bound-parabolic (51)
        O...h-N: upper-bound-parabolic (51)
        O...H-x: upper-bound-parabolic (51)
        Inter-chain: upper-bound-parabolic (12)
        O...H-x (too close!): upper-bound-parabolic (6)
        O...H-x: upper-bound-parabolic (6)
      - Range of distance target values: 1.8, 3.4 (Å)
      - Histogram of distance target values
      - Histogram of discrepancy in distance target values
      - Distance restraints per residue
        Chain_ID: A
        None
        Chain_ID: B
        Chain_ID: C
        Chain_ID: D
      - Distance restraints on contact map
        Chain_ID_1: B - Chain_ID_2: B
        Chain_ID_1: C - Chain_ID_2: C
        None
        Chain_ID_1: D - Chain_ID_2: D
        None
        Chain_ID_1: B - Chain_ID_2: C
        Chain_ID_1: B - Chain_ID_2: D
        Chain_ID_1: C - Chain_ID_2: D
        None

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 9, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 115, Sequence coverage: 93.0%
- Total number of restraints: 176
- Total number of restraints per polymer type: 176
- Weight of restraints: 1.0 (176)
- Potential type of restraints: square-well-parabolic (176)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords DNA BINDING PROTEIN, dinucleotide formation, pRN1 primase, quaternary structure of the helix bundle domain, synergistic effect

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	757	636	84.0
¹³C chemical shifts	560	376	67.1
¹⁵N chemical shifts	123	104	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	228	204	89.5
¹³C chemical shifts	230	104	45.2
¹⁵N chemical shifts	110	97	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	529	432	81.7
¹³C chemical shifts	330	272	82.4
¹⁵N chemical shifts	13	7	53.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	38	79.2
¹³C chemical shifts	45	33	73.3
¹⁵N chemical shifts	3	3	100.0

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BMRB: 34290

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 2. functional pRN1 primase/DNA Complex, entity 2, : 1 : 4 entities Detail

Experiments performed 36 experiments Detail

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