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Open data
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Basic information
Entry | Database: PDB / ID: 1b4v | ||||||
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Title | CHOLESTEROL OXIDASE FROM STREPTOMYCES | ||||||
![]() | PROTEIN (CHOLESTEROL OXIDASE) | ||||||
![]() | OXIDOREDUCTASE / FLAVOENZYME / STEROID METABOLISM | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vrielink, A. / Yue, Q.K. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.3 KB | Display | ![]() |
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PDB format | ![]() | 94.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.7 KB | Display | ![]() |
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Full document | ![]() | 462.3 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b8sC ![]() 1cboC ![]() 1cc2C ![]() 3coxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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) ![]() |
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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: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 % |