+Open data
-Basic information
Entry | Database: PDB / ID: 3cnj | ||||||
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Title | Cholesterol oxidase from Streptomyces sp. F359W mutant (0.95A) | ||||||
Components | Cholesterol oxidase | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / FLAVIN / OXYGEN TUNNEL / CHOLESTEROL OXIDASE / Cholesterol metabolism / FAD / Flavoprotein / Lipid metabolism / Secreted / 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.95 Å | ||||||
Authors | Lyubimov, A.Y. / Brammer, L. / Vrielink, A. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The binding and release of oxygen and hydrogen peroxide are directed by a hydrophobic tunnel in cholesterol oxidase Authors: Chen, L. / Lyubimov, A.Y. / Brammer, L. / Vrielink, A. / Sampson, N.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cnj.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cnj.ent.gz | 220.5 KB | Display | PDB format |
PDBx/mmJSON format | 3cnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cnj ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cnj | HTTPS FTP |
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-Related structure data
Related structure data | 1mxtS 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: 54520.262 Da / Num. of mol.: 1 / Mutation: F359W Source method: isolated from a genetically manipulated source Details: FAD COFACTOR NON-COVALENTLY BOUND TO THE ENZYME / Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: SA-COO / Gene: choA / Plasmid: PCO202 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P12676, cholesterol oxidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.94 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 8000, MANGANESE SULFATE, CACODYLATE (PH 5.2), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 28, 2005 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→46.67 Å / Num. obs: 270322 / % possible obs: 96.3 % / Redundancy: 4.22 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 0.95→0.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 67.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1MXT Resolution: 0.95→46.67 Å / Num. parameters: 48651 / Num. restraintsaints: 71611 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: HYDROGEN ATOMS REFINED USING THE "RIDING" MODEL, WITH BOND LENGTH AND ANGLE CONSTRAINTS. HYDROGEN ATOMS ARE NOT INCLUDED IN THE DEPOSITED COORDINATE FILE. Close contacts are caused by ...Details: HYDROGEN ATOMS REFINED USING THE "RIDING" MODEL, WITH BOND LENGTH AND ANGLE CONSTRAINTS. HYDROGEN ATOMS ARE NOT INCLUDED IN THE DEPOSITED COORDINATE FILE. Close contacts are caused by partial waters in close proximity to alternate conformations of disordered residues. They were modeled manually and their positions were confirmed through several rounds of refinement.
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Refine analyze | Num. disordered residues: 101 / Occupancy sum hydrogen: 3545.79 / Occupancy sum non hydrogen: 4549.37 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→46.67 Å
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Refine LS restraints |
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