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Yorodumi- PDB-2a1m: Crystal structure of ferrous dioxygen complex of wild-type cytoch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a1m | ||||||
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Title | Crystal structure of ferrous dioxygen complex of wild-type cytochrome P450cam | ||||||
Components | Cytochrome P450-cam | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / CYP / dioxygen complex / oxy | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Nagano, S. / Poulos, T.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystallographic study on the dioxygen complex of wild-type and mutant cytochrome P450cam. Implications for the dioxygen activation mechanism Authors: Nagano, S. / Poulos, T.L. #1: Journal: J.Biol.Chem. / Year: 2005 Title: Crystal Structures of the Ferrous Dioxygen Complex of Wild-type Cytochrome P450eryF and Its Mutants, A245S and A245T: INVESTIGATION OF THE PROTON TRANSFER SYSTEM IN P450eryF Authors: Nagano, S. / Cupp-Vickery, J.R. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a1m.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a1m.ent.gz | 145.4 KB | Display | PDB format |
PDBx/mmJSON format | 2a1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/2a1m ftp://data.pdbj.org/pub/pdb/validation_reports/a1/2a1m | HTTPS FTP |
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-Related structure data
Related structure data | 2a1nC 2a1oC 1dz4S 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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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46688.012 Da / Num. of mol.: 2 / Mutation: C334A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00183, camphor 5-monooxygenase |
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-Non-polymers , 6 types, 445 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-TRS / | #7: 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: 2.1 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG 4000, potassium chloride, Tris-HCl, D-camphor, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 11, 2004 / Details: confocal mirror |
Radiation | Monochromator: Osmic's confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.82 Å / Num. obs: 41808 / % possible obs: 90.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.9 Å2 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 1.9 / % possible all: 83.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DZ4 Resolution: 2.1→47.82 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 148961.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.8109 Å2 / ksol: 0.354386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→47.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.14 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 20
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Xplor file |
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