+Open data
-Basic information
Entry | Database: PDB / ID: 1b4v | ||||||
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Title | CHOLESTEROL OXIDASE FROM STREPTOMYCES | ||||||
Components | PROTEIN (CHOLESTEROL OXIDASE) | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM | ||||||
Function / homology | Function and homology information cholesterol oxidase / cholesterol oxidase activity / steroid Delta-isomerase / steroid delta-isomerase activity / cholesterol catabolic process / flavin adenine dinucleotide binding / extracellular region Similarity search - Function | ||||||
Biological species | Streptomyces sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Vrielink, A. / Yue, Q.K. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Crystal structure determination of cholesterol oxidase from Streptomyces and structural characterization of key active site mutants. Authors: Yue, Q.K. / Kass, I.J. / Sampson, N.S. / Vrielink, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b4v.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b4v.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 1b4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b4v ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b4v | HTTPS FTP |
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-Related structure data
Related structure data | 1b8sC 1cboC 1cc2C 3coxS S: Starting model for refinement C: citing same article (ref.) |
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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: 54969.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (natural) Streptomyces sp. (bacteria) / References: UniProt: P12676, cholesterol oxidase |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE OF CHOLESTEROL OXIDASE FROM STREPTOMYCES SP FOUND IN THE SEQUENCE DATA BASE IS A ...THE SEQUENCE OF CHOLESTERO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.2 Details: PRECIPITANT CONDITIONS: 10- 12% PEG 8000, 100MM SODIUM CACODYLATE PH 5.2, 75MM MNSO4 PROTEIN CONCENTRATION 8.5MG/ML, VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 115 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 1, 1996 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22.3 Å / Num. obs: 62747 / % possible obs: 87.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 0.31 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 2 / % possible all: 30.9 |
Reflection | *PLUS Num. measured all: 402969 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3COX Resolution: 1.5→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 12.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / % reflection Rfree: 10.1 % |