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- PDB-5f08: Structure of Transcriptional Regulatory Repressor Protein - EthR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5f08 | ||||||||||||
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Title | Structure of Transcriptional Regulatory Repressor Protein - EthR from Mycobacterium tuberculosis in complex with compound 14 at 1.92A resolution | ||||||||||||
![]() | HTH-type transcriptional regulator EthR | ||||||||||||
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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 / ![]() ![]() 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 | ![]() | 53.2 KB | Display | ![]() |
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PDB format | ![]() | 36.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5eyrC ![]() 5ezgC ![]() 5ezhC ![]() 5f04C ![]() 5f0cC ![]() 5f0fC ![]() 5f0hC ![]() 5f1jC ![]() 5f27C ![]() 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
#1: Protein | Mass: 25259.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ethR, etaR, MT3970 / Production host: ![]() ![]() ![]() |
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#2: Chemical | ChemComp-5TG / ~{ |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % |
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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: 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![]() | |||||||||||||||||||||||||||
Reflection | Resolution: 1.92→53.97 Å / Num. obs: 19677 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Net I/σ(I): 23.2 / Num. measured all: 247645 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1T56 Resolution: 1.92→38.16 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2215 / WRfactor Rwork: 0.1885 / FOM work R set: 0.852 / SU B: 3.03 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1349 / SU Rfree: 0.1307 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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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: 102.35 Å2 / Biso mean: 34.962 Å2 / Biso min: 16.07 Å2
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Refinement step | Cycle: final / Resolution: 1.92→38.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Total num. of bins used: 20
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