BMRB Entry 17419
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17419
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Title: NMR STRUCTURE OF THE CYTIDINE REPRESSOR DNA BINDING DOMAIN IN PRESENCE OF OPERATOR HALF-SITE DNA PubMed: 21688840
Deposition date: 2011-01-20 Original release date: 2011-08-03
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:
HTH-TYPE_TRANSCRIPTIONAL_REPRESSOR_CYTR, polymer, 67 residues, 7402.684 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):
HTH-TYPE_TRANSCRIPTIONAL_REPRESSOR_CYTR: MKAKKQETAATMKDVALKAK
VSTATVSRALMNPDKVSQAT
RNRVEKAAREVGYLPQPMGR
NVKRNES
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 169 |
| 15N chemical shifts | 62 |
| 1H chemical shifts | 372 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR | 1 |
Entities:
Entity 1, HTH-TYPE TRANSCRIPTIONAL REPRESSOR CYTR 67 residues - 7402.684 Da.
| 1 | MET | LYS | ALA | LYS | LYS | GLN | GLU | THR | ALA | ALA | ||||
| 2 | THR | MET | LYS | ASP | VAL | ALA | LEU | LYS | ALA | LYS | ||||
| 3 | VAL | SER | THR | ALA | THR | VAL | SER | ARG | ALA | LEU | ||||
| 4 | MET | ASN | PRO | ASP | LYS | VAL | SER | GLN | ALA | THR | ||||
| 5 | ARG | ASN | ARG | VAL | GLU | LYS | ALA | ALA | ARG | GLU | ||||
| 6 | VAL | GLY | TYR | LEU | PRO | GLN | PRO | MET | GLY | ARG | ||||
| 7 | ASN | 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
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
sample_3: 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%
sample_conditions_1: ionic strength: 0.0570 M; pH: 6.0; pressure: 1 atm; temperature: 308 K
sample_conditions_2: ionic strength: 0.0570 Not defined; 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_3 | 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 | 17634 |
| 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