+Open data
-Basic information
Entry | Database: PDB / ID: 3wrm | ||||||
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Title | Crystal structure of P450cam | ||||||
Components | Camphor 5-monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Metal-binding | ||||||
Function / homology | Function and homology information camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Kishimoto, A. / Takagi, K. / Amano, A. / Sakurai, K. / Mizushima, T. / Shimada, H. | ||||||
Citation | Journal: To be published Title: Structure of P450cam intermedite Authors: Kishimoto, A. / Takagi, K. / Amano, A. / Sakurai, K. / Katayama, Y. / Aminaka, R. / Ito, M. / Mizushima, T. / Shimada, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wrm.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wrm.ent.gz | 144 KB | Display | PDB format |
PDBx/mmJSON format | 3wrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wrm_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3wrm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3wrm_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 3wrm_validation.cif.gz | 50.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wr/3wrm ftp://data.pdbj.org/pub/pdb/validation_reports/wr/3wrm | HTTPS FTP |
-Related structure data
Related structure data | 3wrhC 3wrjC 3wrkC 3wrlC 3l63S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 47548.945 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00183, camphor 5-monooxygenase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.6 % / Mosaicity: 0.587 ° / Mosaicity esd: 0.003 ° |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 50mM Tris-HCl, 200mM KCl, 20-30% PEG 4000, 1mM Camphor, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jan 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 57598 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.95→1.98 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 9.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L63 Resolution: 1.95→39.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2305 / WRfactor Rwork: 0.1775 / FOM work R set: 0.849 / SU B: 3.605 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1785 / SU Rfree: 0.1648 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.48 Å2 / Biso mean: 18.616 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→39.18 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3094 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.951→2.002 Å / Total num. of bins used: 20
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