BMRBj - BMREntryMaster

Found 1 Document (0.634 seconds)

BMRB: 16635

4NC7

Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase

Authors

Motackova, V., Sanderova, H., Zidek, L., Novacek, J., Padrta, P., Svenkova, A., Jonak, J., Krasny, L., Sklenar, V.

Assembly

N delta

Entity

1. N delta (polymer, Thiol state: not present), 99 monomers, 11751.95 Da Detail

GIKQYSQEEL KEMALVEIAH ELFEEHKKPV PFQELLNEIA SLLGVKKEEL GDRIAQFYTD LNIDGRFLAL SDQTWGLRSW YPYDQLDEET QLEHHHHHH

Formula weight

11751.95 Da

Source organism

Bacillus subtilis

Exptl. method

solution NMR

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts, coupling_constants, RDCs

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 96.2 %, Completeness (bb): 95.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	96.2 % (1167 of 1213)	96.1 % (608 of 633)	96.2 % (455 of 473)	97.2 % (104 of 107)
Backbone	95.9 % (564 of 588)	95.0 % (190 of 200)	96.2 % (281 of 292)	96.9 % (93 of 96)
Sidechain	96.7 % (695 of 719)	96.5 % (418 of 433)	96.7 % (266 of 275)	100.0 % (11 of 11)
Aromatic	90.6 % (116 of 128)	90.6 % (58 of 64)	90.3 % (56 of 62)	100.0 % (2 of 2)
Methyl	100.0 % (104 of 104)	100.0 % (52 of 52)	100.0 % (52 of 52)

1. N delta

GIKQYSQEEL KEMALVEIAH ELFEEHKKPV PFQELLNEIA SLLGVKKEEL GDRIAQFYTD LNIDGRFLAL SDQTWGLRSW YPYDQLDEET QLEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
5	N_delta		0.0 ~ 0.0 mM
6	sodium chloride	natural abundance	10 mM
7	sodium azide	natural abundance	50 uM
8	phosphate buffer	natural abundance	20 mM
9	filamentous Pf1 bacteriophage	natural abundance	14.29 mg/mL

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
10	N_delta		0.0 ~ 0.0 mM
11	sodium chloride	natural abundance	10 mM
12	sodium azide	natural abundance	50 uM
13	phosphate buffer	natural abundance	20 mM
14	polyacrylamide gel	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	direct	1.0

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	direct	1.0

Referencing offset: -0.22 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	direct	1.0

Referencing offset: 0.04 ppm, Outliers: 4 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	liquid anhydrous ammonia	nitrogen	na	direct	1.0

Referencing offset: -0.22 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KRC, Strand ID: A Detail

Coupling constant

87 J values in 1 lists
Field strength (¹H) 600 MHz, Pressure 1 atm, Temperature 301 K, pH 6.6 Detail

Release date

2010-05-04

Citation

Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs
Motackova, V., Sanderova, H., Zidek, L., Novacek, J., Padrta, P., Svenkova, A., Korelusova, J., Jonak, J., Krasny, L., Sklenar, V.
Proteins (2010), 78, 1807-1810, PubMed 20310067 , DOI 10.1002/prot.22708 , Abstract

Related entities 1. N delta, : 1 : 2 : 2 : 55 entities Detail

Experiments performed 26 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

2 2D 1H-13C HMQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

3 3D CBCA(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

4 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

5 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

6 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

8 3D HNHA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

11 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

12 (HB)CB(CGCD)HD

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

13 2D 1H-15N IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
5	N_delta		0.0 ~ 0.0 mM
6	sodium chloride	natural abundance	10 mM
7	sodium azide	natural abundance	50 uM
8	phosphate buffer	natural abundance	20 mM
9	filamentous Pf1 bacteriophage	natural abundance	14.29 mg/mL

14 2D HN[C]-S3E

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
5	N_delta		0.0 ~ 0.0 mM
6	sodium chloride	natural abundance	10 mM
7	sodium azide	natural abundance	50 uM
8	phosphate buffer	natural abundance	20 mM
9	filamentous Pf1 bacteriophage	natural abundance	14.29 mg/mL

15 2D (H)CACO-IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
5	N_delta		0.0 ~ 0.0 mM
6	sodium chloride	natural abundance	10 mM
7	sodium azide	natural abundance	50 uM
8	phosphate buffer	natural abundance	20 mM
9	filamentous Pf1 bacteriophage	natural abundance	14.29 mg/mL

16 2D 13C-coupled 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
5	N_delta		0.0 ~ 0.0 mM
6	sodium chloride	natural abundance	10 mM
7	sodium azide	natural abundance	50 uM
8	phosphate buffer	natural abundance	20 mM
9	filamentous Pf1 bacteriophage	natural abundance	14.29 mg/mL

17 2D 1H-15N IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
10	N_delta		0.0 ~ 0.0 mM
11	sodium chloride	natural abundance	10 mM
12	sodium azide	natural abundance	50 uM
13	phosphate buffer	natural abundance	20 mM
14	polyacrylamide gel	natural abundance	5 %

18 2D HN[C]-S3E

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
10	N_delta		0.0 ~ 0.0 mM
11	sodium chloride	natural abundance	10 mM
12	sodium azide	natural abundance	50 uM
13	phosphate buffer	natural abundance	20 mM
14	polyacrylamide gel	natural abundance	5 %

19 2D (H)CACO-IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
10	N_delta		0.0 ~ 0.0 mM
11	sodium chloride	natural abundance	10 mM
12	sodium azide	natural abundance	50 uM
13	phosphate buffer	natural abundance	20 mM
14	polyacrylamide gel	natural abundance	5 %

20 2D 13C-coupled 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
10	N_delta		0.0 ~ 0.0 mM
11	sodium chloride	natural abundance	10 mM
12	sodium azide	natural abundance	50 uM
13	phosphate buffer	natural abundance	20 mM
14	polyacrylamide gel	natural abundance	5 %

21 2D 13C-detected CON

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

22 2D 13C-detected CON

Instrument

Bruker Avance - 600 MHz

Sample

State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
5	N_delta		0.0 ~ 0.0 mM
6	sodium chloride	natural abundance	10 mM
7	sodium azide	natural abundance	50 uM
8	phosphate buffer	natural abundance	20 mM
9	filamentous Pf1 bacteriophage	natural abundance	14.29 mg/mL

23 2D 1H-15N IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

24 2D HN[C]-S3E

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

25 2D (H)CACO-IPAP

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

26 2D 13C-coupled 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 301 K, pH 6.6

#	Name	Isotope labeling	Concentration
1	N_delta		0.0 ~ 0.0 mM
2	sodium chloride	natural abundance	10 mM
3	sodium azide	natural abundance	50 uM
4	phosphate buffer	natural abundance	20 mM

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts, RDC exptl data	bmr16635_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

None

Non-standard residues

None

Content subtype: bmr16635_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1272		97.0 (chain: 1, length: 99)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 99, Sequence coverage: 97.0%
- Total number of assignments
  - ¹H chemical shifts: 715
  - ¹³C chemical shifts: 452
  - ¹⁵N chemical shifts: 105
- Completeness of assignments
  - Entity_assemble_ID: 1
- 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: 1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	633	609	96.2
¹³C chemical shifts	473	452	95.6
¹⁵N chemical shifts	110	105	95.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	200	192	96.0
¹³C chemical shifts	198	187	94.4
¹⁵N chemical shifts	96	92	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	433	417	96.3
¹³C chemical shifts	275	265	96.4
¹⁵N chemical shifts	14	13	92.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	53	53	100.0
¹³C chemical shifts	53	53	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	58	90.6
¹³C chemical shifts	62	56	90.3
¹⁵N chemical shifts	2	2	100.0

Keywords delta subunit, gram-positive bacteria, nuclear magnetic resonance, RNA polymerase, structural homologues

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Found 1 Document (0.634 seconds)

BMRB: 16635

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. N delta, : 1 : 2 : 2 : 55 entities Detail

Experiments performed 26 experiments Detail

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