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Yorodumi- PDB-6f50: CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE DOUBLE VARIANT V88I/L99V -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f50 | ||||||
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Title | CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE DOUBLE VARIANT V88I/L99V | ||||||
Components | Steroid Delta-isomerase | ||||||
Keywords | ISOMERASE / Ksi | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Dunstan, M. / Currin, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: ACS Catal / Year: 2018 Title: Engineering the "Missing Link" in Biosynthetic (-)-Menthol Production: Bacterial Isopulegone Isomerase. Authors: Currin, A. / Dunstan, M.S. / Johannissen, L.O. / Hollywood, K.A. / Vinaixa, M. / Jervis, A.J. / Swainston, N. / Rattray, N.J.W. / Gardiner, J.M. / Kell, D.B. / Takano, E. / Toogood, H.S. / Scrutton, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f50.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f50.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 6f50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/6f50 ftp://data.pdbj.org/pub/pdb/validation_reports/f5/6f50 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13791.647 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: ksi / Production host: Escherichia coli (E. coli) / References: UniProt: P07445, steroid Delta-isomerase #2: 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: 2.27 Å3/Da / Density % sol: 45.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 10-25% PEG3350 with 0.2 M MgCl2; ii) 10-25% PEG3350 with 0.2 M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 180 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→95.4 Å / Num. obs: 17276 / % possible obs: 99.9 % / Redundancy: 6.5 % / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2→2.1 Å |
-Processing
Software |
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Refinement | Resolution: 2→29.192 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 23.75
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 114.11 Å2 / Biso mean: 32.9813 Å2 / Biso min: 10.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→29.192 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: -5.8702 Å / Origin y: -18.4632 Å / Origin z: 23.9284 Å
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Refinement TLS group |
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