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Yorodumi- PDB-1lfk: Crystal structure of OxyB, a Cytochrome P450 Implicated in an Oxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lfk | ||||||
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Title | Crystal structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling Reaction During Vancomycin Biosynthesis | ||||||
Components | P450 monooxygenaseCytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / OXIDATIVE PHENOL COUPLING REACTION P450 VANCOMYCIN | ||||||
Function / homology | Function and homology information vancomycin biosynthetic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Amycolatopsis orientalis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å | ||||||
Authors | Pylypenko, O. / Zerbe, K. / Vitali, F. / Zhang, W. / Vrijbloed, J.W. / Robinson, J.A. / Schlichting, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal Structure of OxyB, a Cytochrome P450 Implicated in an Oxidative Phenol Coupling Reaction during Vancomycin Biosynthesis. Authors: Zerbe, K. / Pylypenko, O. / Vitali, F. / Zhang, W. / Rouset, S. / Heck, M. / Vrijbloed, J.W. / Bischoff, D. / Bister, B. / Sussmuth, R.D. / Pelzer, S. / Wohlleben, W. / Robinson, J.A. / Schlichting, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lfk.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lfk.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 1lfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lfk ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lfk | HTTPS FTP |
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-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: 44429.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis orientalis (bacteria) / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RN04 |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.45 Å3/Da / Density % sol: 49.46 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Ammonium Sulphate, K-Hepes, DTE, pottasium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→28.8 Å / Num. all: 166149 / Num. obs: 49572 / % possible obs: 98.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.1 Å2 / Rsym value: 0.066 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.255 / % possible all: 99.5 |
Reflection | *PLUS % possible obs: 98.7 % / Num. measured all: 166149 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 99.7 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 5.3 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→28.8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2494352.16 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.7601 Å2 / ksol: 0.361238 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.8 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→28.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 1.8 Å |