BMRB Entry 36187

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36187
MolProbity Validation Chart

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Title:
Solution Structure of the DNA-Binding 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, 103 residues, 11693.313 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: .

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AGIPDGTTRRRRGTARPGSK AAKLREAAIKTLKRHNAAIK SSELQKEIEKESGLEIPNMT TFMQSLIKMYPEVKKPYRGQ YILEGEIESAESANELEHHH HHH

Data sets:
Data typeCount
13C chemical shifts424
15N chemical shifts98
1H chemical shifts703

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 103 residues - 11693.313 Da.

1   ALAGLYILEPROASPGLYTHRTHRARGARG
2   ARGARGGLYTHRALAARGPROGLYSERLYS
3   ALAALALYSLEUARGGLUALAALAILELYS
4   THRLEULYSARGHISASNALAALAILELYS
5   SERSERGLULEUGLNLYSGLUILEGLULYS
6   GLUSERGLYLEUGLUILEPROASNMETTHR
7   THRPHEMETGLNSERLEUILELYSMETTYR
8   PROGLUVALLYSLYSPROTYRARGGLYGLN
9   TYRILELEUGLUGLYGLUILEGLUSERALA
10   GLUSERALAASNGLULEUGLUHISHISHIS
11   HISHISHIS

Samples:

sample_1: Rok, [U-13C;U-15N], 1 mM; H2O 90%; D2O, [U-2H], 10%

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

Experiments:

NameSampleSample stateSample conditions
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1

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:

  • Bruker 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