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Found 1 Document (0.637 seconds)

BMRB: 34287

6GT7

NMR structure of the free helix bundle domain from the functional pRN1 primase

Authors

Boudet, J., Lipps, G., Allain, F.

Assembly

functional pRN1 primase

Entity

1. functional pRN1 primase (polymer, Thiol state: all disulfide bound), 115 monomers, 13503.53 Da Detail

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

Formula weight

13503.53 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS29:SG	1:CYS42:SG

Source organism

Sulfolobus islandicus

Exptl. method

solution NMR

Refine. method

simulated annealing with the SANDER module of AMBER12

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.8 %, Completeness: 74.1 %, Completeness (bb): 71.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	74.1 % (1064 of 1435)	75.7 % (573 of 757)	69.1 % (387 of 560)	88.1 % (104 of 118)
Backbone	71.5 % (486 of 680)	78.1 % (178 of 228)	60.5 % (207 of 342)	91.8 % (101 of 110)
Sidechain	77.6 % (673 of 867)	74.7 % (395 of 529)	83.3 % (275 of 330)	37.5 % (3 of 8)
Aromatic	87.5 % (84 of 96)	89.6 % (43 of 48)	84.4 % (38 of 45)	100.0 % (3 of 3)
Methyl	91.2 % (124 of 136)	91.2 % (62 of 68)	91.2 % (62 of 68)

1. entity 1

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 1.2 mM [U-99% 13C; U-99% 15N] helix bundle domain, 0.9 mM [U-99% 15N] helix bundle domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.7 mM [U-100% 13C] helix bundle domain, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	13C helix bundle domain	[U-100% 13C]		0.7 mM
5	NaCl	natural abundance		50 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	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	1.0

Referencing offset: 0.23 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	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	1.0

Referencing offset: 0.23 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	1.0
¹⁵N	water	protons	4.7 ppm	internal	direct	1.0

Referencing offset: 0.17 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 6GT7, Strand ID: A Detail

Release date

2018-10-24

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

Entries sharing articles BMRB: 2 entries Detail

  BMRB: 34291 released on 2018-10-16
    Title NMR structure of the DNA-bound helix bundle domain from the functional pRN1 primase
  BMRB: 34290 released on 2018-09-25
    Title Hybrid structure of the pRN1 helix bundle domain in complex with DNA and 2 ATP molecules

Related entities 1. functional pRN1 primase, : 1 : 4 entities Detail

Experiments performed 10 experiments Detail

1 15N-NOESY-HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 1.2 mM [U-99% 13C; U-99% 15N] helix bundle domain, 0.9 mM [U-99% 15N] helix bundle domain, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

2 13Cali-NOESY-HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

3 13Caro-NOESY-HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

4 13Cali-HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.7 mM [U-100% 13C] helix bundle domain, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	13C helix bundle domain	[U-100% 13C]		0.7 mM
5	NaCl	natural abundance		50 mM

5 13Caro-HSQC

Instrument

Bruker AVANCE III - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.7 mM [U-100% 13C] helix bundle domain, 100% D2O

#	Name	Isotope labeling	Type	Concentration
4	13C helix bundle domain	[U-100% 13C]		0.7 mM
5	NaCl	natural abundance		50 mM

6 15N-HSQC

Instrument

Bruker AVANCE III HD - 900 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

7 3D HNCACB

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

8 3D CBCA(CO)NH

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

9 3D HNCA

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

10 3D HN(CO)CA

Instrument

Bruker AVANCE III - 700 MHz

Sample

#	Name	Isotope labeling	Concentration
1	13C, 15N helix bundle domain	[U-99% 13C; U-99% 15N]	1.2 mM
2	15N helix bundle domain	[U-99% 15N]	0.9 mM
3	NaCl	natural abundance	50 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_34287_6gt7.nef
Input source #2: Coordindates	6gt7.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
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)
A:284:CYS:SG	A:297:CYS:SG	oxidized, CA 58.35, CB 40.865 ppm	oxidized, CB 38.934 ppm	2.038

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

None

Non-standard residues

None

Sequence alignments

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

--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	115	0	0	100.0

Content subtype: combined_34287_6gt7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1041		94.8 (chain: A, length: 115)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2800 (1)	noe	89.6 (chain: A, length: 115)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	196 (1)	noe	55.7 (chain: A, length: 115)
3	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	216 (1)	hbond	67.0 (chain: A, length: 115)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	174 (174)	.	88.7 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 94.8%
- Total number of assignments
  - ¹³C chemical shifts: 370
  - ¹H chemical shifts: 569
  - ¹⁵N chemical shifts: 102
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	560	370	66.1
¹H chemical shifts	757	567	74.9
¹⁵N chemical shifts	123	102	82.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	230	97	42.2
¹H chemical shifts	228	178	78.1
¹⁵N chemical shifts	110	99	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	330	273	82.7
¹H chemical shifts	529	389	73.5
¹⁵N chemical shifts	13	3	23.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	69	63	91.3
¹H chemical shifts	69	63	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	45	38	84.4
¹H chemical shifts	48	43	89.6
¹⁵N chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 89.6%
- Total number of restraints: 2800
- Weight of restraints: 1.0 (2800)
- Potential type of restraints: upper-bound-parabolic (2800)
- Range of distance target values: 2.36, 5.99 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 55.7%
  - Total number of restraints: 196
  - Weight of restraints: 1.0 (196)
  - Potential type of restraints: upper-bound-parabolic (196)
  - Range of distance target values: 3.0, 6.0 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 67.0%
    - Total number of restraints: 216
    - Weight of restraints: 1.0 (216)
    - Potential type of restraints: upper-bound-parabolic (216)
    - 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
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 88.7%
- Total number of restraints: 174
- Total number of restraints per polymer type: 174
- Weight of restraints: 1.0 (174)
- Potential type of restraints: square-well-parabolic (174)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords dinucleotide formation, functional pRN1 primase, replication initiation, transferase, unusual archaeo-eukaryotic primase

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Found 1 Document (0.637 seconds)

BMRB: 34287

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 2 entries Detail

Related entities 1. functional pRN1 primase, : 1 : 4 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 6 contents Detail