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Yorodumi- PDB-2a15: X-ray Crystal Structure of RV0760 from Mycobacterium Tuberculosis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a15 | ||||||
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Title | X-ray Crystal Structure of RV0760 from Mycobacterium Tuberculosis at 1.68 Angstrom Resolution | ||||||
Components | HYPOTHETICAL PROTEIN Rv0760c | ||||||
Keywords | UNKNOWN FUNCTION / beta-alpha-barrel / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | ||||||
Authors | Garen, C.R. / Cherney, M.M. / 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.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a15.cif.gz | 44.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a15.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 2a15.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a15_validation.pdf.gz | 439.5 KB | Display | wwPDB validaton report |
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Full document | 2a15_full_validation.pdf.gz | 440.4 KB | Display | |
Data in XML | 2a15_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 2a15_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a15 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a15 | HTTPS FTP |
-Related structure data
Related structure data | 2z76C 2z77C 2z7aC 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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Unit cell |
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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: y-x,y,2/3-z |
-Components
#1: Protein | Mass: 15256.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SIMILARITY WITH PDB IDs 1BUQ, 1CQS, 1E3R, 1E3V, 1OH0 ETC. SUGGESTS THAT THIS PROTEIN IS KETOSTEROID ISOMERASE Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0760 / Production host: Escherichia coli (E. coli) / References: UniProt: P71817 |
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#2: Chemical | ChemComp-NCA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.28 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.6 M Na, K Phosphate, 100mM Hepes buffer pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.68→48.17 Å / Num. all: 21399 / Num. obs: 21399 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 7.6 % / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: the model was obtained from a SAD solution from the data collected on SeMet variant of the same protein. Resolution: 1.68→48.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.813 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.088 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.639 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→48.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.68→1.724 Å / Total num. of bins used: 20
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