+Open data
-Basic information
Entry | Database: PDB / ID: 6r1p | ||||||
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Title | EthR ligand complex | ||||||
Components | HTH-type transcriptional regulator EthR | ||||||
Keywords | DNA BINDING PROTEIN / Transcriptional regulator Tuberculosis TetR Inhibitor | ||||||
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 / Resolution: 1.8 Å | ||||||
Authors | Pohl, E. / Tatum, N. | ||||||
Citation | Journal: J Phys Chem Lett / Year: 2019 Title: Relative Binding Energies Predict Crystallographic Binding Modes of Ethionamide Booster Lead Compounds. Authors: Tatum, N.J. / Duarte, F. / Kamerlin, S.C.L. / Pohl, E. #1: Journal: Org.Biomol.Chem. / Year: 2017 Title: New active leads for tuberculosis booster drugs by structure-based drug discovery. Authors: Tatum, N.J. / Liebeschuetz, J.W. / Cole, J.C. / Frita, R. / Herledan, A. / Baulard, A.R. / Willand, N. / Pohl, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6r1p.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r1p.ent.gz | 39.5 KB | Display | PDB format |
PDBx/mmJSON format | 6r1p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r1p_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6r1p_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6r1p_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 6r1p_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/6r1p ftp://data.pdbj.org/pub/pdb/validation_reports/r1/6r1p | HTTPS FTP |
-Related structure data
Related structure data | 6r1sC 5nimS 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
#1: Protein | Mass: 23781.705 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ethR, etaR, Rv3855 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WMC1 |
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#2: Chemical | ChemComp-JPH / |
#3: 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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10 mM MES, 1.4-1.6M Ammonium sulphate / PH range: 6-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→86 Å / Num. obs: 44875 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rsym value: 0.055 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Num. unique obs: 6620 / Rsym value: 0.49 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NIM Resolution: 1.8→29.55 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.178 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.425 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→29.55 Å
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Refine LS restraints |
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