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Yorodumi- PDB-1nff: Crystal structure of Rv2002 gene product from Mycobacterium tuber... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nff | ||||||
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Title | Crystal structure of Rv2002 gene product from Mycobacterium tuberculosis | ||||||
Components | Putative oxidoreductase Rv2002 | ||||||
Keywords | OXIDOREDUCTASE / Directed evolution / GFP / SDR / hydroxysteroid dehydrogenase / structural genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | Function and homology information 3alpha(or 20beta)-hydroxysteroid dehydrogenase / androstan-3-alpha,17-beta-diol dehydrogenase activity / steroid catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / steroid metabolic process / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yang, J.K. / Park, M.S. / Waldo, G.S. / Suh, S.W. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis Authors: Yang, J.K. / Park, M.S. / Waldo, G.S. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nff.cif.gz | 112.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nff.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 1nff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nff ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nff | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27101.729 Da / Num. of mol.: 2 / Mutation: I6T, V47M, T69K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) References: UniProt: P69167, UniProt: P9WGT1*PLUS, 3alpha(or 20beta)-hydroxysteroid dehydrogenase #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: 1.86 Å3/Da / Density % sol: 33.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3000, calcium acetate, Tris-HCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 40259 / Num. obs: 40259 / % possible obs: 99.7 % / Biso Wilson estimate: 16.6 Å2 |
Reflection shell | Resolution: 1.8→1.9 Å / % possible all: 99.7 |
Reflection | *PLUS Num. measured all: 280336 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1827572.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.2448 Å2 / ksol: 0.389283 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→19.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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