+Open data
-Basic information
Entry | Database: PDB / ID: 7f7n | |||||||||
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Title | Solution structure of apo-WhiB4 from Mycobacterium tuberculosis | |||||||||
Components | Transcriptional regulator WhiB4 | |||||||||
Keywords | DNA BINDING PROTEIN / apo-WhiB4 / helix-turn-helix domain / intrinsically disordered domain | |||||||||
Function / homology | Function and homology information dinitrosyl-iron complex binding / protein-disulfide reductase (NAD(P)H) activity / cell wall / protein-disulfide reductase activity / cell redox homeostasis / 4 iron, 4 sulfur cluster binding / negative regulation of DNA-templated transcription / DNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Xia, B. / Duan, B. | |||||||||
Funding support | China, 2items
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Citation | ||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f7n.cif.gz | 784.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f7n.ent.gz | 658.2 KB | Display | PDB format |
PDBx/mmJSON format | 7f7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/7f7n ftp://data.pdbj.org/pub/pdb/validation_reports/f7/7f7n | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14305.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: whiB4, Rv3681c / Production host: Escherichia coli (E. coli) / References: UniProt: P9WF39 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.4 mM [U-100% 13C; U-100% 15N] WhiB4, 95% H2O/5% D2O Details: The NMR samples containing 0.4 mM reduced apo-WhiB4 in 50 mM Tris-HCl buffer (pH 7.0) with 95% H2O/5% D2O, along with 50 mM NaCl, 20 mM DTT, 0.03% NaN3, 0.01% DSS and 5% tablet of EDTA-free ...Details: The NMR samples containing 0.4 mM reduced apo-WhiB4 in 50 mM Tris-HCl buffer (pH 7.0) with 95% H2O/5% D2O, along with 50 mM NaCl, 20 mM DTT, 0.03% NaN3, 0.01% DSS and 5% tablet of EDTA-free protease inhibitor cocktail (Roche) Label: 15N_13C_sample / Solvent system: 95% H2O/5% D2O |
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Sample | Conc.: 0.4 mM / Component: WhiB4 / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Details: 50 mM Tris-HCl buffer, 50 mM NaCl, 20 mM DTT, 0.03% NaN3, 0.01% DSS, and 5% tablet of EDTA-free protease inhibitor cocktail (Roche) Ionic strength: 50 mM NaCl mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 2 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |