+Open data
-Basic information
Entry | Database: PDB / ID: 5n7o | ||||||
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Title | EthR2 in complex with SMARt-420 compound | ||||||
Components | Probable transcriptional regulatory protein | ||||||
Keywords | TRANSCRIPTION / Repressor / complex / inhibitor | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wohlkonig, A. / Wintjens, R. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2017 Title: Structural analysis of the interaction between spiroisoxazoline SMARt-420 and the Mycobacterium tuberculosis repressor EthR2. Authors: Wohlkonig, A. / Remaut, H. / Moune, M. / Tanina, A. / Meyer, F. / Desroses, M. / Steyaert, J. / Willand, N. / Baulard, A.R. / Wintjens, R. #1: Journal: Science / Year: 2017 Title: Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420 Authors: Blondiaux, N. / Moune, M. / Desroses, M. / Frita, R. / Flipo, M. / Mathys, V. / Soetaert, K. / Kiass, M. / Delorme, V. / Djaout, K. / Trebosc, V. / Kemmer, C. / Wintjens, R. / Wohlkonig, A. ...Authors: Blondiaux, N. / Moune, M. / Desroses, M. / Frita, R. / Flipo, M. / Mathys, V. / Soetaert, K. / Kiass, M. / Delorme, V. / Djaout, K. / Trebosc, V. / Kemmer, C. / Wintjens, R. / Wohlkonig, A. / Antoine, R. / Huot, L. / Hot, D. / Coscolla, M. / Feldmann, J. / Gagneux, S. / Locht, C. / Brodin, P. / Gitzinger, M. / Deprez, B. / Willand, N. / Baulard, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n7o.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n7o.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 5n7o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/5n7o ftp://data.pdbj.org/pub/pdb/validation_reports/n7/5n7o | HTTPS FTP |
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-Related structure data
Related structure data | 5n1iS S: Starting model for refinement |
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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: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 11 - 201 / Label seq-ID: 31 - 221
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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, LH57_00450 / Plasmid: pET15b Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O53623 #2: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.21 % |
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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 pH 4.2 and 15% PEG-MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→60 Å / Num. obs: 18592 / % possible obs: 98.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.998 / Rsym value: 0.118 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 5.9 / Num. unique obs: 2925 / CC1/2: 0.97 / Rsym value: 0.52 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N1I Resolution: 2.3→57.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.282 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.238 / 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: 36.571 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→57.67 Å
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Refine LS restraints |
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