BMRB Entry 17729
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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/BMR17729
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Title: Structure of the DNA complex of the C-Terminal domain of Ler PubMed: 22114557
Deposition date: 2011-06-23 Original release date: 2011-12-06
Authors: Cordeiro, Tiago; Schimdt, Holger; Grisienger, Christian; Pons, Miquel; Cordeiro, Tiago
Citation: Cordeiro, Tiago; Schimdt, Holger; Madrid, Cristina; Juarez, Antonio; Bernado, Pau; Grisienger, Christian; Garcia, Jesus; Pons, Miquel. "Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler" PLoS Pathog. 7, e1002380-. (2011).
Assembly members:
CT-Ler, polymer, 57 residues, 6703.430 Da.
LeeH_A, polymer, 15 residues, 6703.430 Da.
LeeH_B, polymer, 15 residues, 6703.430 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):
CT-Ler: SHHHHHHSMGNSSKGVYYRN
EEGQTWSGVGRQPRWLKEAL
LNGMKKEDFLVKDTEEE
LeeH_A: GCGATAATTGATAGG
LeeH_B: CCTATCAATTATCGC
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 151 |
| 15N chemical shifts | 59 |
| 1H chemical shifts | 637 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CT-Ler | 1 |
| 2 | LeeH_A | 2 |
| 3 | LeeH_B | 3 |
Entities:
Entity 1, CT-Ler 57 residues - 6703.430 Da.
| 1 | SER | HIS | HIS | HIS | HIS | HIS | HIS | SER | MET | GLY | ||||
| 2 | ASN | SER | SER | LYS | GLY | VAL | TYR | TYR | ARG | ASN | ||||
| 3 | GLU | GLU | GLY | GLN | THR | TRP | SER | GLY | VAL | GLY | ||||
| 4 | ARG | GLN | PRO | ARG | TRP | LEU | LYS | GLU | ALA | LEU | ||||
| 5 | LEU | ASN | GLY | MET | LYS | LYS | GLU | ASP | PHE | LEU | ||||
| 6 | VAL | LYS | ASP | THR | GLU | GLU | GLU |
Entity 2, LeeH_A 15 residues - 6703.430 Da.
| 1 | DG | DC | DG | DA | DT | DA | DA | DT | DT | DG | ||||
| 2 | DA | DT | DA | DG | DG |
Entity 3, LeeH_B 15 residues - 6703.430 Da.
| 1 | DC | DC | DT | DA | DT | DC | DA | DA | DT | DT | ||||
| 2 | DA | DT | DC | DG | DC |
Samples:
sample_1: CT-Ler, [U-100% 13C; U-100% 15N], 1 mM; LeeH_A 2 mM; LeeH_B 2 mM; sodium phosphate 20 mM; sodium chloride 20 mM; sodium azide 0.01 %(w/v); EDTA 0.2 mM; H2O 90%; D2O 10%
sample_2: CT-Ler, [U-100% 13C; U-100% 15N], 1 mM; LeeH_A 2 mM; LeeH_B 2 mM; sodium phosphate 20 mM; sodium chloride 150 mM; sodium azide 0.01 %(w/v); EDTA 0.2 mM; D2O 100%
sample_3: CT-Ler, [U-10% 13C; U-100% 15N], 1 mM; LeeH_A 2 mM; LeeH_B 2 mM; sodium phosphate 20 mM; sodium chloride 150 mM; sodium azide 0.01 % (w/v); EDTA 0.2 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 150 mM; pH: 5.7; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC aliphatic | sample_3 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aliphatic | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H (13C-ed) NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H (13C-fil) NOESY | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-1H (15N/13C-fil) NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 15N/13C-fil/13c-ed- NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H (13C-fil) TOCSY | sample_2 | isotropic | sample_conditions_1 |
Software:
NMRPipe, Delaglio, Zhengrong and Bax - Processing
TOPSPIN, Bruker Biospin - NMR spectra acquisition
CYANA, Guntert, Mumenthaler and Wuthrich - Structure Calculation
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - Energy water refinement
CARA, Keller and Wuthrich - Chemical shift assignment
TALOS, Cornilescu, Delaglio and Bax - Prediction of Protein Phi and Psi Angles Using a Chemical Shift Database
CRYSOL, Svergun D.I., Barberato C. and Koch M.H.J. - Fitting to experimental scattering curves
HADDOCK, Alexandre Bonvin - Data-driven docking using CNS as structure calculation engine
AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - molecular dynamics refinement
Procheck, Laskowski and MacArthur - Quality assessment
NMR spectrometers:
- Bruker Avance 600 MHz
- Bruker Avance 700 MHz
- Bruker Avance 800 MHz
- Bruker Avance 900 MHz
Related Database Links:
| PDB | |
| DBJ | BAB38011 BAI28393 BAI32361 BAI37557 BAT37610 |
| EMBL | CAC81843 CAG17510 CAI43893 CAR47961 CAS11516 |
| GB | AAC31533 AAC38364 AAG58852 AAK26696 AAL57523 |
| REF | NP_312615 WP_001055727 WP_001055728 WP_001310359 WP_001339878 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts