+Open data
-Basic information
Entry | Database: PDB / ID: 1nfq | ||||||
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Title | Rv2002 gene product from Mycobacterium tuberculosis | ||||||
Components | Putative oxidoreductase Rv2002 | ||||||
Keywords | OXIDOREDUCTASE / Directed evolution / SDR / GFP / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 1nfq.cif.gz | 190.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nfq.ent.gz | 160.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nfq ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nfq | 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.: 4 / 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 | ChemComp-NAI / #3: Chemical | ChemComp-AOI / #4: 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: 2.47 Å3/Da / Density % sol: 49.82 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG400, HEPES, pH 7.5, 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: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. all: 40358 / Num. obs: 40358 / % possible obs: 99.5 % / Biso Wilson estimate: 20.3 Å2 |
Reflection shell | Resolution: 2.4→2.5 Å / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 133031 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 99.9 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.91 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 303293.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.3161 Å2 / ksol: 0.359412 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→19.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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