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Yorodumi- PDB-5f04: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5f04 | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 3 at 1.84A 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 / cytosol Similarity search - Function | ||||||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å | ||||||||||||
Authors | Surade, S. / Blaszczyk, M. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | United Kingdom, United States, 3items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f04.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f04.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f04_validation.pdf.gz | 727.2 KB | Display | wwPDB validaton report |
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Full document | 5f04_full_validation.pdf.gz | 728.3 KB | Display | |
Data in XML | 5f04_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5f04_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f0/5f04 ftp://data.pdbj.org/pub/pdb/validation_reports/f0/5f04 | HTTPS FTP |
-Related structure data
Related structure data | 5eyrC 5ezgC 5ezhC 5f08C 5f0cC 5f0fC 5f0hC 5f1jC 5f27C 1t56S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 25259.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, etaR, MT3970 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC0, UniProt: P9WMC1*PLUS |
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-Non-polymers , 5 types, 78 molecules
#2: Chemical | ChemComp-5TB / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.48 % |
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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 | |||||||||||||||||||||||||||
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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: 1.84→86.12 Å / Num. obs: 22766 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.016 / Net I/σ(I): 27.9 / Num. measured all: 286725 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T56 Resolution: 1.84→54.466 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.26 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.33 Å2 / Biso mean: 34.8161 Å2 / Biso min: 14.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.84→54.466 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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