BMRB Entry 17634

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17634
MolProbity Validation Chart

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Title:
Structure of the Cytidine Repressor DNA-Binding Domain; an alternate calculation
Deposition date:
2011-05-10
Original release date:
2011-06-22
Authors:
Moody, C.; Tretyachenko-Ladokhina, V.; Senear, D.; Cocco, M.
Citation:

Citation: Moody, Colleen; Tretyachenko-Ladokhina, Vira; Laue, Thomas; Senear, Donald; Cocco, Melanie. "Multiple conformations of the cytidine repressor DNA-binding domain coalesce to one upon recognition of a specific DNA surface."  Biochemistry 50, 6622-6632 (2011).
PubMed: 21688840

Assembly members:

Assembly members:
CytR_DBD, polymer, 66 residues, 5053.923 Da.

Natural source:

Natural source:   Common Name: E.coli   Taxonomy ID: 562   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Escherichia coli

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pSS584DBD

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CytR_DBD: KAKKQETAATMKDVALKAKV STATVSRALMNPDKVSQATR NRVEKAAREVGYLPQPMGRN VKRNES

Data sets:
Data typeCount
13C chemical shifts169
15N chemical shifts62
1H chemical shifts364

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1CytR_DBD1

Entities:

Entity 1, CytR_DBD 66 residues - 5053.923 Da.

1   LYSALALYSLYSGLNGLUTHRALAALATHR
2   METLYSASPVALALALEULYSALALYSVAL
3   SERTHRALATHRVALSERARGALALEUMET
4   ASNPROASPLYSVALSERGLNALATHRARG
5   ASNARGVALGLULYSALAALAARGGLUVAL
6   GLYTYRLEUPROGLNPROMETGLYARGASN
7   VALLYSARGASNGLUSER

Samples:

sample_1: HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR, [U-15N], 0.411 mM; ATTTATGCAACGCA DNA 1.14 mM; sodium phosphate 50 mM; sodium chloride 30 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_2: HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR, [U-13C; U-15N], 1 mM; ATTTATGCAACGCA DNA 1.2 mM; sodium phosphate 50 mM; sodium chloride 30 mM; EDTA 1 mM; H2O 90%; D2O 10%

sample_4: HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR, [U-15N], 0.4 mM; ATTTATGCAACGCA DNA 0.6 mM; sodium phosphate 50 mM; sodium chloride 30 mM; EDTA 1 mM; C12E5 PEG/HEXANOL 4%; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.0570 M; pH: 6.0; pressure: 1 atm; temperature: 308 K

sample_conditions_2: ionic strength: 0.0570 M; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
HCCH-TOCSYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_4anisotropicsample_conditions_2

Software:

X-PLOR NIH, SCHWIETERS, KUSZEWSKI, TJ - refinement

VNMR, Varian - structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - structure solution

ANALYSIS_-_CCPN, CCPN - structure solution

NMR spectrometers:

  • VARIAN INOVA 800 MHz

Related Database Links:

BMRB 17419
PDB
DBJ BAB38284 BAE77376 BAG79747 BAI27816 BAI33290
EMBL CAA27318 CAP78391 CAQ34285 CAR00910 CAR05564
GB AAA24417 AAB03066 AAC76916 AAG59129 AAN45445
REF NP_312888 NP_418369 NP_709738 WP_000644802 WP_000644884
SP P0ACN7 P0ACN8 P0ACN9 P0ACP0
AlphaFold P0ACN7 P0ACN8 P0ACN9 P0ACP0

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