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Yorodumi- PDB-2inx: Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2inx | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 2,6-difluorophenol | ||||||
Components | Steroid delta-isomerase | ||||||
Keywords | ISOMERASE / KSI / enzyme / active site / charge distribution / hydrogen bond | ||||||
Function / homology | Function and homology information steroid Delta-isomerase / steroid delta-isomerase activity / steroid metabolic process Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Martinez Caaveiro, J.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Sigala, P. / Kraut, D. / Herschlag, D. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. Authors: Sigala, P.A. / Kraut, D.A. / Caaveiro, J.M. / Pybus, B. / Ruben, E.A. / Ringe, D. / Petsko, G.A. / Herschlag, D. #1: Journal: PLOS Biol. / Year: 2006 Title: Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole Authors: Kraut, D. / Sigala, P. / Pybus, B. / Liu, C.W. / Ringe, D. / Petsko, G.A. / Herschlag, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2inx.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2inx.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 2inx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/in/2inx ftp://data.pdbj.org/pub/pdb/validation_reports/in/2inx | HTTPS FTP |
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-Related structure data
Related structure data | 3cpoC 2b32 S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 14547.515 Da / Num. of mol.: 1 / Mutation: D40N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase |
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#2: Chemical | ChemComp-FFP / |
#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: 2.07 Å3/Da / Density % sol: 40.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium sulphate 1.4 M, 2-propanol 6.5% protein concentration 25 mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004 |
Radiation | Monochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.4 Å / Num. all: 19911 / Num. obs: 19274 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.079 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 8.9 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1890 / Rsym value: 0.374 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2B32 2b32 Resolution: 1.5→47.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.648 / SU ML: 0.062 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.095 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.929 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→47.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.537 Å / Total num. of bins used: 20
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