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Yorodumi- PDB-1w02: Crystal structure of mutant enzyme Y16F/D103L of ketosteroid isom... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w02 | ||||||
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Title | Crystal structure of mutant enzyme Y16F/D103L of ketosteroid isomerase from Pseudomonas putida biotype B | ||||||
Components | STEROID DELTA-ISOMERASE | ||||||
Keywords | ISOMERASE / CONESHELL / CLOSED BARREL / CURVED B-SHEET | ||||||
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: 2.3 Å | ||||||
Authors | Jang, D.S. / Choi, K.Y. | ||||||
Citation | Journal: Biochem.J. / Year: 2004 Title: Structural Double-Mutant Cycle Analysis of a Hydrogen Bond Network in Ketosteroid Isomerase from Pseudomonas Putida Biotype B. Authors: Jang, D.S. / Cha, H.J. / Cha, S.S. / Hong, B.H. / Ha, N.C. / Lee, J.Y. / Oh, B.H. / Lee, H.S. / Choi, K.Y. #1: Journal: Biochemistry / Year: 2000 Title: Contribution of the Hydrogen-Bond Network Involving a Tyrosine Triad in the Active Site to the Structure and Function of a Highly Proficient Ketosteroid Isomerase from Pseudomonas Putida Biotype B Authors: Kim, D.H. / Jang, D.S. / Nam, G.H. / Choi, G. / Kim, J.S. / Ha, N.C. / Kim, M.S. / Oh, B.H. / Choi, K.Y. #2: Journal: J.Biol.Chem. / Year: 1999 Title: Crystal Structure of Delta(5)-3-Ketosteroid Isomerase from Pseudomonas Testosteroni in Complex with Equilenin Settles the Correct Hydrogen Bonding Scheme for Transition State Stabilization Authors: Cho, H.S. / Ha, N.C. / Choi, G. / Kim, H.J. / Lee, D. / Oh, K.S. / Kim, K.S. / Lee, W. / Choi, K.Y. / Oh, B.H. #3: Journal: Biochemistry / Year: 1998 Title: Crystal Structure and Enzyme Mechanism of Delta(5)-3-Ketosteroid Isomerase from Pseudomonas Testosteroni Authors: Cho, H.S. / Choi, G. / Choi, K.Y. / Oh, B.H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w02.cif.gz | 39 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w02.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/1w02 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/1w02 | 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: 14530.571 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445, steroid Delta-isomerase |
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#2: Water | ChemComp-HOH / |
Compound details | ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.34 % |
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Crystal grow | pH: 4.6 / Details: SODIUM ACETATE, AMMONIUM ACETATE, pH 4.60 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 6746 / % possible obs: 91.7 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.15→2.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.226 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.06 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 844504.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 43.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.06 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
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Xplor file |
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