+Open data
-Basic information
Entry | Database: PDB / ID: 1b8s | ||||||
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Title | CHOLESTEROL OXIDASE FROM STREPTOMYCES GLU361GLN MUTANT | ||||||
Components | PROTEIN (CHOLESTEROL OXIDASE) | ||||||
Keywords | FLAVOENZYME / STEROID METABOLISM / OXIDOREDUCTASE | ||||||
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 / OTHER / Resolution: 1.65 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 | 1b8s.cif.gz | 121.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b8s.ent.gz | 91 KB | Display | PDB format |
PDBx/mmJSON format | 1b8s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b8s_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 1b8s_full_validation.pdf.gz | 470.4 KB | Display | |
Data in XML | 1b8s_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1b8s_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/1b8s ftp://data.pdbj.org/pub/pdb/validation_reports/b8/1b8s | HTTPS FTP |
-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: 54968.691 Da / Num. of mol.: 1 / Mutation: GLU361GLN Source method: isolated from a genetically manipulated source Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (gene. exp.) Streptomyces sp. (bacteria) / Plasmid: PCO219 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / 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: Dec 1, 1997 |
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: 1.65→24 Å / Num. obs: 49835 / % possible obs: 91.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 35.1 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 2 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 2 / % possible all: 52.5 |
Reflection | *PLUS Num. measured all: 281106 / Rmerge(I) obs: 0.05 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.65→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: 12.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.73 Å / Rfactor Rfree error: 0.027 / 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 Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 12.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.489 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.46 |