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Yorodumi- PDB-2fe6: P450CAM from Pseudomonas putida reconstituted with manganic proto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fe6 | ||||||
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Title | P450CAM from Pseudomonas putida reconstituted with manganic protoporphyrin IX | ||||||
Components | Cytochrome P450-cam | ||||||
Keywords | OXIDOREDUCTASE / MONO-OXYGENASE / HEME / Manganic / Substrate-Free | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.5 Å | ||||||
Authors | von Koenig, K. / Makris, T.M. / Sligar, S.G. / Schlichting, I. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2006 Title: The status of high-valent metal oxo complexes in the P450 cytochromes. Authors: Makris, T.M. / Koenig, K. / Schlichting, I. / Sligar, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fe6.cif.gz | 105.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fe6.ent.gz | 78.4 KB | Display | PDB format |
PDBx/mmJSON format | 2fe6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fe6_validation.pdf.gz | 813.4 KB | Display | wwPDB validaton report |
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Full document | 2fe6_full_validation.pdf.gz | 821.8 KB | Display | |
Data in XML | 2fe6_validation.xml.gz | 21.4 KB | Display | |
Data in CIF | 2fe6_validation.cif.gz | 32.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/2fe6 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/2fe6 | HTTPS FTP |
-Related structure data
Related structure data | 2ferC 2feuC 1yrdS 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: 47548.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pet28 / Production host: Escherichia coli (E. coli) / Strain (production host): AW804 (DE3) / References: UniProt: P00183, camphor 5-monooxygenase |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-MNR / |
#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: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 7.5 MG/ML P450, 50 MM TRIS, 125 MM KCL, 13.5-15% PEG8000, 50 MM DTE, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.93 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 29, 2005 / Details: Si(111) monochromator, dynamically bendable mirror |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→18 Å / Num. obs: 84598 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rsym value: 0.086 / Net I/σ(I): 7.01 |
Reflection shell | Resolution: 1.4→1.5 Å / Mean I/σ(I) obs: 2.38 / Num. unique all: 30433 / Num. unique obs: 18162 / Rsym value: 0.24 / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1yrd Resolution: 1.5→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: initial parameters for Mn porphyrin IX from: Suslick, K.S. et al. (1991), Inorg. Chem. 30, 2311-17.
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Solvent computation | Bsol: 52.904 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.327 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.6 Å / Num. reflection obs: 26508 | ||||||||||||||||||||||||||||
Xplor file |
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