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Yorodumi- PDB-3fzw: Crystal Structure of Ketosteroid Isomerase D40N-D103N from Pseudo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fzw | ||||||
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Title | Crystal Structure of Ketosteroid Isomerase D40N-D103N from Pseudomonas putida (pKSI) with bound equilenin | ||||||
Components | Steroid Delta-isomerase | ||||||
Keywords | ISOMERASE / KSI / enzyme catalysis / hydrogen bond / transition state / oxyanion hole / Lipid metabolism / Steroid metabolism | ||||||
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 / molecular replacement / Resolution: 1.32 Å | ||||||
Authors | Caaveiro, J.M.M. / Ringe, D. / Petsko, G.A. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Hydrogen bond coupling in the ketosteroid isomerase active site. Authors: Sigala, P.A. / Caaveiro, J.M. / 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. #2: 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. / Kraut, D. / Caaveiro, J.M.M. / Pybus, B. / Ruben, E.A. / 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 | 3fzw.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fzw.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 3fzw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fzw_validation.pdf.gz | 949.2 KB | Display | wwPDB validaton report |
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Full document | 3fzw_full_validation.pdf.gz | 953.4 KB | Display | |
Data in XML | 3fzw_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 3fzw_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/3fzw ftp://data.pdbj.org/pub/pdb/validation_reports/fz/3fzw | HTTPS FTP |
-Related structure data
Related structure data | 2inxS S: Starting model for refinement |
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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: 14546.530 Da / Num. of mol.: 2 / Mutation: D40N, D103N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07445, steroid Delta-isomerase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-IPA / | #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: 54.13 % |
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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%, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979462 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2007 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979462 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→50 Å / Num. all: 68149 / Num. obs: 68149 / % possible obs: 94 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.006 / Net I/σ(I): 10.337 |
Reflection shell | Resolution: 1.32→1.37 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.373 / Num. unique all: 5090 / Χ2: 1.011 / % possible all: 70.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2INX Resolution: 1.32→55.05 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.206 / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.88 / SU B: 1.816 / SU ML: 0.033 / SU R Cruickshank DPI: 0.048 / SU Rfree: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.048 / 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 max: 45.06 Å2 / Biso mean: 19.12 Å2 / Biso min: 10.17 Å2
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Refinement step | Cycle: LAST / Resolution: 1.32→55.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.316→1.351 Å / Total num. of bins used: 20
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