[English] 日本語
Yorodumi- PDB-1c7h: CRYSTAL STRUCTURE OF A MUTANT R75A IN KETOSTEROID ISOMERASE FROM ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c7h | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF A MUTANT R75A IN KETOSTEROID ISOMERASE FROM PSEDOMONAS PUTIDA BIOTYPE B | ||||||
Components | DELTA-5-3-KETOSTEROID ISOMERASE | ||||||
Keywords | ISOMERASE / KSI / R75A | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Nam, G.H. / Kim, D.H. / Jang, D.S. / Choi, G. / Ha, N.C. / Oh, B.H. / Choi, K.Y. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Roles of active site aromatic residues in catalysis by ketosteroid isomerase from Pseudomonas putida biotype B. Authors: Kim, D.H. / Nam, G.H. / Jang, D.S. / Choi, G. / Joo, S. / Kim, J.S. / Oh, B.H. / Choi, K.Y. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1c7h.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1c7h.ent.gz | 24.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c7h_validation.pdf.gz | 417.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1c7h_full_validation.pdf.gz | 423.1 KB | Display | |
Data in XML | 1c7h_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1c7h_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c7h ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c7h | HTTPS FTP |
-Related structure data
Related structure data | 1opyS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 14462.384 Da / Num. of mol.: 1 / Mutation: R75A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: BIOTYPE B / Plasmid: PKK / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 / Details: pH 4.6 | |||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 295 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 4081 / % possible obs: 95.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3 / Rsym value: 0.291 / % possible all: 91 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OPY Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |