[English] 日本語
Yorodumi- PDB-3vgn: Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vgn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas putida (pKSI) with bound 3-fluoro-4-nitrophenol | ||||||
Components | Steroid Delta-isomerase | ||||||
Keywords | ISOMERASE / hydrogen bond / KSI / enzyme catalysis / transition state / oxyanion hole | ||||||
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: 1.3 Å | ||||||
Authors | Caaveiro, J.M.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Sigala, P.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Quantitative dissection of hydrogen bond-mediated proton transfer in the ketosteroid isomerase active site Authors: Sigala, P.A. / Fafarman, A.T. / Schwans, J.P. / Fried, S.D. / Fenn, T.D. / Caaveiro, J.M.M. / Pybus, B. / Ringe, D. / Petsko, G.A. / Boxer, S.G. / Herschlag, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3vgn.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3vgn.ent.gz | 101.1 KB | Display | PDB format |
PDBx/mmJSON format | 3vgn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vgn_validation.pdf.gz | 454.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3vgn_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 3vgn_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 3vgn_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/3vgn ftp://data.pdbj.org/pub/pdb/validation_reports/vg/3vgn | HTTPS FTP |
-Related structure data
Related structure data | 3owsC 3fzwS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14547.515 Da / Num. of mol.: 2 / Mutation: D40N 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.45 % / Mosaicity: 0.965 ° |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.4M Ammonium sulphate, 6-7% 2-propanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.82656 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2005 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.82656 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→35 Å / Num. all: 55738 / Num. obs: 55738 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.006 / Net I/σ(I): 10.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FZW Resolution: 1.3→33.25 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.2498 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7999 / SU B: 2.252 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0635 / SU Rfree: 0.0631 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 106.63 Å2 / Biso mean: 22.6604 Å2 / Biso min: 9.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→33.25 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
|