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Yorodumi- PDB-2z76: X-ray crystal structure of RV0760c from Mycobacterium tuberculosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z76 | ||||||
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Title | X-ray crystal structure of RV0760c from Mycobacterium tuberculosis at 1.82 Angstrom resolution | ||||||
Components | Putative steroid isomerase | ||||||
Keywords | ISOMERASE / alpha+beta conical barrel / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Cherney, M.M. / Garen, C.R. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2008 Title: Crystal structure of Mycobacterium tuberculosis Rv0760c at 1.50 A resolution, a structural homolog of Delta(5)-3-ketosteroid isomerase. Authors: Cherney, M.M. / Garen, C.R. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z76.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z76.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 2z76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/2z76 ftp://data.pdbj.org/pub/pdb/validation_reports/z7/2z76 | HTTPS FTP |
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-Related structure data
Related structure data | 2a15SC 2z77C 2z7aC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Two molecules in the asymmetric unit is a biological assembly |
-Components
#1: Protein | Mass: 15256.006 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0760c, MT0785 / Plasmid: pGST-0760c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P71817 #2: Chemical | #3: Chemical | ChemComp-LDA / | #4: Chemical | ChemComp-MPD / ( | #5: 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: 2.68 Å3/Da / Density % sol: 54.07 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 8% PEG 8000, 0.1M Sodium acetate, 0.02% LDAO, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. all: 28871 / Num. obs: 28871 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.035 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.27 / Rsym value: 0.471 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2A15 Resolution: 1.82→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.467 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.82→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.82→1.869 Å / Total num. of bins used: 20
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