[English] 日本語
Yorodumi- PDB-5f0h: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f0h | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 28 at 1.99A resolution | ||||||||||||
Components | HTH-type transcriptional regulator EthR | ||||||||||||
Keywords | TRANSCRIPTION / EthR / repressor / Mycobacterium tuberculosis | ||||||||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis CDC1551 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å | ||||||||||||
Authors | Surade, S. / Blaszczyk, M. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | United Kingdom, United States, 3items
| ||||||||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2016 Title: A fragment merging approach towards the development of small molecule inhibitors of Mycobacterium tuberculosis EthR for use as ethionamide boosters. Authors: Nikiforov, P.O. / Surade, S. / Blaszczyk, M. / Delorme, V. / Brodin, P. / Baulard, A.R. / Blundell, T.L. / Abell, C. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5f0h.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5f0h.ent.gz | 36.9 KB | Display | PDB format |
PDBx/mmJSON format | 5f0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f0h ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f0h | HTTPS FTP |
---|
-Related structure data
Related structure data | 5eyrC 5ezgC 5ezhC 5f04C 5f08C 5f0cC 5f0fC 5f1jC 5f27C 1t56S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 25259.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis CDC1551 (bacteria) Gene: ethR, etaR, MT3970 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC0, UniProt: P9WMC1*PLUS |
---|---|
#2: Chemical | ChemComp-5TC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Ammonium sulphate, Glycerol, MES / PH range: 6.3 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97943 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2013 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97943 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.99→53.82 Å / Num. obs: 17617 / % possible obs: 99.9 % / Redundancy: 12.7 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Net I/σ(I): 25.7 / Num. measured all: 223127 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T56 Resolution: 1.99→53.82 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2118 / WRfactor Rwork: 0.182 / FOM work R set: 0.8295 / SU B: 3.822 / SU ML: 0.103 / SU R Cruickshank DPI: 0.1531 / SU Rfree: 0.1415 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.05 Å2 / Biso mean: 37.981 Å2 / Biso min: 15.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.99→53.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.99→2.042 Å / Total num. of bins used: 20
|