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Yorodumi- PDB-3p6w: Crystal Structure of Cytochrome P450cam crystallized in the prese... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3p6w | ||||||
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Title | Crystal Structure of Cytochrome P450cam crystallized in the presence of a tethered substrate analog AdaC3-Etg-Boc | ||||||
Components | Camphor 5-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / P450cam / camphor / tethered substrate analog / open conformation | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Lee, Y.-T. / Wilson, R.F. / Glazer, E.C. / Goodin, D.B. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Cytochrome P450cam crystallized in the presence of a tethered substrate analog AdaC3-Etg-Boc Authors: Lee, Y.-T. / Glazer, E.C. / Wilson, R.F. / Goodin, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p6w.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p6w.ent.gz | 72.2 KB | Display | PDB format |
PDBx/mmJSON format | 3p6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/3p6w ftp://data.pdbj.org/pub/pdb/validation_reports/p6/3p6w | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 46556.816 Da / Num. of mol.: 1 / Mutation: C334A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase |
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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: 2.47 Å3/Da / Density % sol: 50.15 % |
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Crystal grow | Temperature: 279 K / Method: sitting-drop vapor diffusion / pH: 6.5 Details: 12-22% PEG 8000, 0.1M Sodium cacodylate, pH 6.5, 0.1-0.2M KCl, sitting-drop vapor diffusion, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97839 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 2007 / Details: RH COATED FLAT MIRROR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97839 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→92.946 Å / Num. all: 27619 / Num. obs: 25134 / % possible obs: 91.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 33.9 Å2 / Rsym value: 0.085 / Net I/σ(I): 9.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2562 / WRfactor Rwork: 0.2011 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8182 / SU B: 5.355 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2602 / SU Rfree: 0.2187 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.02 Å2 / Biso mean: 34.3977 Å2 / Biso min: 18.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.152 Å / Total num. of bins used: 20
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