BMRB Entry 36186

Name: Solution Structure of the DNA complex of the C-terminal Domain of Rok
Published: 2020-07-15

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PDB ID: 5zux
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36186
MolProbity Validation Chart

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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 DNA complex of the C-terminal Domain of Rok

Deposition date:

2018-05-08

Original release date:

2020-07-15

Authors:

Xia, B.; Duan, B.

Citation:

Citation: Duan, B.; Ding, P.; Hughes, T.; Navarre, W.; Liu, J.; Xia, B.. "How bacterial xenogeneic silencer rok distinguishes foreign from self DNA in its resident genome." Nucleic Acids Res. 46, 10514-10529 (2018).
PubMed: 30252102

Assembly members:

Assembly members:
entity_1, polymer, 92 residues, 10638.262 Da.
entity_2, polymer, 18 residues, 5513.615 Da.

Natural source:

Natural source: Common Name: Bacillus subtilis Taxonomy ID: 224308 Superkingdom: Bacteria Kingdom: not available Genus/species: Bacillus Bacillus subtilis

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GTTRRRRGTARPGSKAAKLR EAAIKTLKRHNAAIKSSELQ KEIEKESGLEIPNMTTFMQS LIKMYPEVKKPYRGQYILEG EIESLEHHHHHH
entity_2: CTAATAACTAGTTATTAG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	355
15N chemical shifts	83
1H chemical shifts	971

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2, 1	2
3	entity_2, 2	2

Entities:

Entity 1, entity_1 92 residues - 10638.262 Da.

1

GLY

THR

ARG

GLY

THR

ALA

2

ARG

PRO

GLY

SER

LYS

ALA

LYS

LEU

ARG

3

GLU

ALA

ILE

LYS

THR

LEU

LYS

ARG

HIS

4

ASN

ALA

ILE

LYS

SER

GLU

LEU

GLN

5

LYS

GLU

ILE

GLU

LYS

GLU

SER

GLY

LEU

GLU

6

ILE

PRO

ASN

MET

THR

PHE

MET

GLN

SER

7

LEU

ILE

LYS

MET

TYR

PRO

GLU

VAL

LYS

8

PRO

TYR

ARG

GLY

GLN

TYR

ILE

LEU

GLU

GLY

9

GLU

ILE

GLU

SER

LEU

GLU

HIS

10

HIS

Entity 2, entity_2, 1 18 residues - 5513.615 Da.

1

DC

DT

DA

DT

DA

DC

DT

DA

2

DG

DT

DA

DT

DA

DG

Samples:

sample_1: Rok, [U-99% 13C; U-99% 15N], 0.5 mM; Seq1, [U-13C;U-15N], 2.5 mM; H2O 90%; D2O, [U-2H], 10%

sample_2: Rok, [U-99% 13C; U-99% 15N], 0.5 mM; Seq1, 1H_12C_14N, 2.5 mM; D2O, [U-2H], 100%

sample_conditions_1: ionic strength: 50 mM; pH: 6.0 .; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.0 .; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D F1-15N/13C filtered, F2-13C edited NOESY	sample_1	isotropic	sample_conditions_2
2D F1, F2-15N/13C-filtered 1H-1H NOESY	sample_1	isotropic	sample_conditions_2

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - peak picking

SANE, Duggan, Legge, Dyson & Wright - chemical shift assignment

NMR spectrometers:

BrukerBruker Avance 500 MHz
Bruker Avance 950 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks