+Open data
-Basic information
Entry | Database: PDB / ID: 6hrw | ||||||
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Title | EthR2 in complex with compound 1 (BDM14272) | ||||||
Components | Probable transcriptional regulatory protein | ||||||
Keywords | DNA BINDING PROTEIN / HELIX-TURN-HELIX / TETR-FAMILY / COMPLEX / INHIBITOR / DRUG DESIGN / TUBERCULOSIS / ETHIONAMIDE | ||||||
Function / homology | Function and homology information transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Wintjens, R. / Wohlkonig, A. / Tanina, A. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2019 Title: A fragment-based approach towards the discovery of N-substituted tropinones as inhibitors of Mycobacterium tuberculosis transcriptional regulator EthR2. Authors: Prevet, H. / Moune, M. / Tanina, A. / Kemmer, C. / Herledan, A. / Frita, R. / Wohlkonig, A. / Bourotte, M. / Villemagne, B. / Leroux, F. / Gitzinger, M. / Baulard, A.R. / Deprez, B. / ...Authors: Prevet, H. / Moune, M. / Tanina, A. / Kemmer, C. / Herledan, A. / Frita, R. / Wohlkonig, A. / Bourotte, M. / Villemagne, B. / Leroux, F. / Gitzinger, M. / Baulard, A.R. / Deprez, B. / Wintjens, R. / Willand, N. / Flipo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hrw.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hrw.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hrw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/6hrw ftp://data.pdbj.org/pub/pdb/validation_reports/hr/6hrw | HTTPS FTP |
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-Related structure data
Related structure data | 6hrxC 6hryC 6hrzC 6hs0C 6hs1C 6hs2C 5n7oS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 0 / Auth seq-ID: 11 - 200 / Label seq-ID: 31 - 220
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-Components
#1: Protein | Mass: 24122.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: Rv0078 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O53623 #2: Chemical | ChemComp-GNK / ( | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 0.2 M NaCl, 0.2 M Na citrate and 15% (W/V) PEG-MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 5, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→30 Å / Num. obs: 15012 / % possible obs: 99.4 % / Redundancy: 6.99 % / Rrim(I) all: 0.235 / Net I/σ(I): 9.65 |
Reflection shell | Resolution: 2.45→2.6 Å / Redundancy: 6.57 % / Mean I/σ(I) obs: 2.04 / Num. unique obs: 2334 / Rrim(I) all: 1.203 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N7O Resolution: 2.45→27.76 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.884 / SU B: 10.895 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.585 / ESU R Free: 0.317 / 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: 32.698 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→27.76 Å
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Refine LS restraints |
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