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Yorodumi- PDB-5n1i: unliganded form of the Mycobacterium tuberculosis repressor EthR2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n1i | |||||||||
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Title | unliganded form of the Mycobacterium tuberculosis repressor EthR2 | |||||||||
Components | Probable transcriptional regulatory protein | |||||||||
Keywords | DNA BINDING PROTEIN / Repressor / EthR / TetR protein family. | |||||||||
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 H37Rv (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Wintjens, R. / Wohlkonig, A. | |||||||||
Citation | 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. #1: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n1i.cif.gz | 83.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n1i.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 5n1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/5n1i ftp://data.pdbj.org/pub/pdb/validation_reports/n1/5n1i | HTTPS FTP |
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-Related structure data
Related structure data | 5icjC 5n1cSC 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: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: 12 - 201 / Label seq-ID: 32 - 221
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-Components
#1: Protein | Mass: 24122.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: PURIFICATION TAG: RESIDUE 1-20 Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: Rv0078, LH57_00450 / Details (production host): CLONAGE SITES: NdeI-BamH1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: O53623 #2: 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: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 200 mM NaCl, 200 mM Na Citrate pH 4.2 and 15%polyethylene glycol monomethylether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98011 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 16231 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 60.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 1.45 |
Reflection shell | Resolution: 2.4→2.54 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2440 / CC1/2: 0.88 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N1C Resolution: 2.4→38.36 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 11.989 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.46 / ESU R Free: 0.283 / 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: 62.589 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→38.36 Å
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Refine LS restraints |
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