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- PDB-5f27: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f27 | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium Tuberculosis in complex with compound 2 at 1.68A resolution | ||||||||||||
![]() | HTH-type transcriptional regulator EthR | ||||||||||||
![]() | TRANSCRIPTION / EthR / repressor / Mycobacterium tuberculosis | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Surade, S. / Blaszczyk, M. / Nikiforov, P.O. / Abell, C. / Blundell, T.L. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 56.8 KB | Display | ![]() |
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PDB format | ![]() | 39.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.3 KB | Display | ![]() |
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Full document | ![]() | 434.3 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5eyrC ![]() 5ezgC ![]() 5ezhC ![]() 5f04C ![]() 5f08C ![]() 5f0cC ![]() 5f0fC ![]() 5f0hC ![]() 5f1jC ![]() 1t56S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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
#1: Protein | Mass: 25259.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.82 % |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.684→84.973 Å / Num. all: 27668 / Num. obs: 27668 / % possible obs: 97.3 % / Redundancy: 8.6 % / Rpim(I) all: 0.028 / Rrim(I) all: 0.081 / Rsym value: 0.076 / Net I/av σ(I): 5.799 / Net I/σ(I): 18.3 / Num. measured all: 238221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T56 Resolution: 1.684→42.487 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.37 / 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: 69 Å2 / Biso mean: 28.4824 Å2 / Biso min: 10.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.684→42.487 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: 10
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