BMRB Entry 16635

Name: Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase
Published: 2010-05-05

Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16635

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

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

Deposition date:

2009-12-16

Original release date:

2010-05-05

Authors:

Motackova, Veronika; Sanderova, Hana; Zidek, Lukas; Novacek, Jiri; Padrta, Petr; Svenkova, Alzbeta; Jonak, Jiri; Krasny, Libor; Sklenar, Vladimir

Citation:

Citation: Motackova, Veronika; Sanderova, Hana; Zidek, Lukas; Novacek, Jiri; Padrta, Petr; Svenkova, Alzbeta; Korelusova, Jana; Jonak, Jiri; Krasny, Libor; Sklenar, Vladimir. "Solution structure of the N-terminal domain of Bacillus subtilis delta subunit of RNA polymerase and its classification based on structural homologs." Proteins 78, 1807-1810 (2010).
PubMed: 20310067

Assembly members:

Assembly members:
N_delta, polymer, 99 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Bacillus subtilis Taxonomy ID: 1423 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacillus subtilis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET22b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
N_delta: GIKQYSQEELKEMALVEIAH ELFEEHKKPVPFQELLNEIA SLLGVKKEELGDRIAQFYTD LNIDGRFLALSDQTWGLRSW YPYDQLDEETQLEHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
coupling_constants
- coupling_constant_list_1
RDCs
- RDC_list_1
- RDC_list_2

Data type	Count
13C chemical shifts	452
15N chemical shifts	105
1H chemical shifts	715
coupling constants	87
residual dipolar couplings	346

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	N_delta	1

Entities:

Entity 1, N_delta 99 residues - Formula weight is not available

1

GLY

ILE

LYS

GLN

TYR

SER

GLN

GLU

LEU

2

LYS

GLU

MET

ALA

LEU

VAL

GLU

ILE

ALA

HIS

3

GLU

LEU

PHE

GLU

HIS

LYS

PRO

VAL

4

PRO

PHE

GLN

GLU

LEU

ASN

GLU

ILE

ALA

5

SER

LEU

GLY

VAL

LYS

GLU

LEU

6

GLY

ASP

ARG

ILE

ALA

GLN

PHE

TYR

THR

ASP

7

LEU

ASN

ILE

ASP

GLY

ARG

PHE

LEU

ALA

LEU

8

SER

ASP

GLN

THR

TRP

GLY

LEU

ARG

SER

TRP

9

TYR

PRO

TYR

ASP

GLN

LEU

ASP

GLU

THR

10

GLN

LEU

GLU

HIS

Samples:

sample_1: N_delta mM; sodium chloride 10 mM; sodium azide 50 uM; phosphate buffer 20 mM

sample_2: N_delta mM; sodium chloride 10 mM; sodium azide 50 uM; phosphate buffer 20 mM; filamentous Pf1 bacteriophage 14.29 mg/ml

sample_3: N_delta mM; sodium chloride 10 mM; sodium azide 50 uM; phosphate buffer 20 mM; polyacrylamide gel 5%

sample_conditions_1: ionic strength: 10 mM; pH: 6.6; pressure: 1 atm; temperature: 301 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HMQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
(HB)CB(CGCD)HD	sample_1	isotropic	sample_conditions_1
2D 1H-15N IPAP	sample_2	anisotropic	sample_conditions_1
2D HN[C]-S3E	sample_2	anisotropic	sample_conditions_1
2D (H)CACO-IPAP	sample_2	anisotropic	sample_conditions_1
2D 13C-coupled 1H-13C HSQC	sample_2	anisotropic	sample_conditions_1
2D 1H-15N IPAP	sample_3	anisotropic	sample_conditions_1
2D HN[C]-S3E	sample_3	anisotropic	sample_conditions_1
2D (H)CACO-IPAP	sample_3	anisotropic	sample_conditions_1
2D 13C-coupled 1H-13C HSQC	sample_3	anisotropic	sample_conditions_1
2D 13C-detected CON	sample_1	isotropic	sample_conditions_1
2D 13C-detected CON	sample_2	anisotropic	sample_conditions_1
2D 1H-15N IPAP	sample_1	isotropic	sample_conditions_1
2D HN[C]-S3E	sample_1	isotropic	sample_conditions_1
2D (H)CACO-IPAP	sample_1	isotropic	sample_conditions_1
2D 13C-coupled 1H-13C HSQC	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRDraw v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.111, Goddard - chemical shift assignment, peak picking

ARIA v2.1, Linge, O'Donoghue and Nilges - NOE assignment

CNS vTENSO, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

X-PLOR, Brunger - refinement

S3EPY, Petr Novak - dipolar coupling determination, peak picking

NMR spectrometers:

Bruker Avance 600 MHz

BMRB	16912 18903 19284
PDB	2KRC 2M4K 4NC7 4NC8
DBJ	BAM55799 BAM59811 BAO93636 GAK81030
EMBL	CAA89869 CAB15744 CCU60814 CEI59524 CEJ79381
GB	AAA22710 ADM39706 ADV94526 AEP88664 AEP92774
REF	NP_391597 WP_003221959 WP_003227609 WP_003235832 WP_003243661
SP	P12464
AlphaFold	P12464