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
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Title: Structure of the Cytidine Repressor DNA-Binding Domain; an alternate calculation PubMed: 21688840
Deposition date: 2011-05-10 Original release date: 2011-06-22
Authors: Moody, C.; Tretyachenko-Ladokhina, V.; Senear, D.; Cocco, M.
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).
Assembly members:
CytR_DBD, polymer, 66 residues, 5053.923 Da.
Natural source: Common Name: E.coli Taxonomy ID: 562 Superkingdom: Bacteria Kingdom: not available Genus/species: Escherichia coli
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
CytR_DBD: KAKKQETAATMKDVALKAKV
STATVSRALMNPDKVSQATR
NRVEKAAREVGYLPQPMGRN
VKRNES
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 169 |
| 15N chemical shifts | 62 |
| 1H chemical shifts | 364 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CytR_DBD | 1 |
Entities:
Entity 1, CytR_DBD 66 residues - 5053.923 Da.
| 1 | LYS | ALA | LYS | LYS | GLN | GLU | THR | ALA | ALA | THR | ||||
| 2 | MET | LYS | ASP | VAL | ALA | LEU | LYS | ALA | LYS | VAL | ||||
| 3 | SER | THR | ALA | THR | VAL | SER | ARG | ALA | LEU | MET | ||||
| 4 | ASN | PRO | ASP | LYS | VAL | SER | GLN | ALA | THR | ARG | ||||
| 5 | ASN | ARG | VAL | GLU | LYS | ALA | ALA | ARG | GLU | VAL | ||||
| 6 | GLY | TYR | LEU | PRO | GLN | PRO | MET | GLY | ARG | ASN | ||||
| 7 | VAL | LYS | ARG | ASN | GLU | SER |
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:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | sample_4 | anisotropic | sample_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 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts