BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 36186

Title: Solution Structure of the DNA complex of the C-terminal Domain of Rok   PubMed: 30252102

Deposition date: 2018-05-08 Original release date: 2020-07-15

Authors: Xia, B.; Duan, B.

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).

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

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

Experimental source:   Production method: chemical synthesis

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

Data typeCount
13C chemical shifts355
15N chemical shifts83
1H chemical shifts971

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_2, 12
3entity_2, 22

Entities:

Entity 1, entity_1 92 residues - 10638.262 Da.

1   GLYTHRTHRARGARGARGARGGLYTHRALA
2   ARGPROGLYSERLYSALAALALYSLEUARG
3   GLUALAALAILELYSTHRLEULYSARGHIS
4   ASNALAALAILELYSSERSERGLULEUGLN
5   LYSGLUILEGLULYSGLUSERGLYLEUGLU
6   ILEPROASNMETTHRTHRPHEMETGLNSER
7   LEUILELYSMETTYRPROGLUVALLYSLYS
8   PROTYRARGGLYGLNTYRILELEUGLUGLY
9   GLUILEGLUSERLEUGLUHISHISHISHIS
10   HISHIS

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

1   DCDTDADADTDADADCDTDA
2   DGDTDTDADTDTDADG

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:

NameSampleSample stateSample conditions
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D F1-15N/13C filtered, F2-13C edited NOESYsample_1isotropicsample_conditions_2
2D F1, F2-15N/13C-filtered 1H-1H NOESYsample_1isotropicsample_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 simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts