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Yorodumi- PDB-5ai1: Crystal structure of ketosteroid isomerase containing Y32F, D40N,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ai1 | ||||||
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Title | Crystal structure of ketosteroid isomerase containing Y32F, D40N, Y57F and Y119F mutations in the equilenin-bound form | ||||||
Components | KETOSTEROID ISOMERASE | ||||||
Keywords | ISOMERASE / KETOSTEROID ISOMERASE / PSEUDOMONAS PUTIDA / EQUILENIN | ||||||
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: 2.103 Å | ||||||
Authors | Cha, H.J. / Jeong, J.H. / Kim, Y.G. | ||||||
Citation | Journal: Mol.Cells / Year: 2015 Title: Contribution of a Low-Barrier Hydrogen Bond to Catalysis is not Significant in Ketosteroid Isomerase. Authors: Jang, D.S. / Choi, G. / Cha, H.J. / Shin, S. / Hong, B.H. / Lee, H.J. / Lee, H.C. / Choi, K.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ai1.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ai1.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ai1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/5ai1 ftp://data.pdbj.org/pub/pdb/validation_reports/ai/5ai1 | HTTPS FTP |
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-Related structure data
Related structure data | 1opyS 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
#1: Protein | Mass: 14499.515 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Variant: BIOTYPE B / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07445 |
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#2: Chemical | ChemComp-EQU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.17 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 0.1M SODIUM ACETATE (PH 4.5), 0.6M AMMONIUM ACETATE, 30% PEG 4,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30.13 Å / Num. obs: 7126 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 26.51 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OPY Resolution: 2.103→30.134 Å / SU ML: 0.26 / σ(F): 1.5 / Phase error: 26.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.103→30.134 Å
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Refine LS restraints |
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LS refinement shell |
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