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Yorodumi- PDB-4v12: Crystal structure of the MSMEG_6754 dehydratase from Mycobacteriu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v12 | ||||||
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Title | Crystal structure of the MSMEG_6754 dehydratase from Mycobacterium smegmatis | ||||||
Components | MAOC LIKE DOMAIN PROTEIN | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | N-terminal of MaoC-like dehydratase / N-terminal half of MaoC dehydratase / MaoC-like dehydratase domain / MaoC like domain / HotDog domain superfamily / Chem-POG / MaoC like domain protein Function and homology information | ||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Blaise, M. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2015 Title: A New Dehydratase Conferring Innate Resistance to Thiacetazone and Intra-Amoebal Survival of Mycobacterium Smegmatis. Authors: Carrere-Kremer, S. / Blaise, M. / Singh, V.K. / Alibaud, L. / Tuaillon, E. / Halloum, I. / Van De Weerd, R. / Guerardel, Y. / Drancourt, M. / Takiff, H. / Geurtsen, J. / Kremer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v12.cif.gz | 151.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4v12.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 4v12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v12_validation.pdf.gz | 448.4 KB | Display | wwPDB validaton report |
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Full document | 4v12_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 4v12_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4v12_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v1/4v12 ftp://data.pdbj.org/pub/pdb/validation_reports/v1/4v12 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37022.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM SMEGMATIS (bacteria) / Plasmid: PET32 EK/LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: A0R724 |
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#2: Chemical | ChemComp-POG / ( |
#3: Chemical | ChemComp-BTB / |
#4: Water | ChemComp-HOH / |
Sequence details | THE ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 6.5, 45% V/V POLYPROPYLENE GLYCOL P 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. obs: 70527 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 16.37 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.8 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.2 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.5→29.297 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 15.87 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→29.297 Å
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Refine LS restraints |
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LS refinement shell |
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