+Open data
-Basic information
Entry | Database: PDB / ID: 3gyi | ||||||
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Title | Cholesterol oxidase from Streptomyces sp. N485D mutant (1.0A) | ||||||
Components | Cholesterol oxidase | ||||||
Keywords | OXIDOREDUCTASE / GMC oxidoreductase / site-directed mutagenesis / hydrophobic tunnel / flavoprotein / Cholesterol metabolism / FAD / 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: 1 Å | ||||||
Authors | Lyubimov, A.Y. / Vrielink, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: A hydrogen-bonding network is important for oxidation and isomerization in the reaction catalyzed by cholesterol oxidase. Authors: Lyubimov, A.Y. / Chen, L. / 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 | 3gyi.cif.gz | 272.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gyi.ent.gz | 218.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/3gyi ftp://data.pdbj.org/pub/pdb/validation_reports/gy/3gyi | HTTPS FTP |
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-Related structure data
Related structure data | 3gyjC 1mxtS 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: 54970.660 Da / Num. of mol.: 1 / Mutation: N485D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: SA-COO / Gene: choA / Production host: Escherichia coli (E. coli) / References: UniProt: P12676, cholesterol oxidase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-SO4 / |
#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: 2.06 Å3/Da / Density % sol: 40.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 9-11% PEG 8000, 75 mM MnSO4, 100 mM 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: BL11-1 / Wavelength: 0.98 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Details: FLAT MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1→30.4 Å / Num. obs: 231276 / % possible obs: 96.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1→1.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 1.5 / % possible all: 58.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 1MXT Resolution: 1→30.4 Å / Num. parameters: 49066 / Num. restraintsaints: 73087 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Num. disordered residues: 175 / Occupancy sum hydrogen: 3488.51 / Occupancy sum non hydrogen: 4514.37 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→30.4 Å
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Refine LS restraints |
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