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Yorodumi- PDB-1akd: CYTOCHROME P450CAM FROM PSEUDOMONAS PUTIDA, COMPLEXED WITH 1S-CAMPHOR -
+Open data
-Basic information
Entry | Database: PDB / ID: 1akd | ||||||
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Title | CYTOCHROME P450CAM FROM PSEUDOMONAS PUTIDA, COMPLEXED WITH 1S-CAMPHOR | ||||||
Components | CYTOCHROME P450CAM | ||||||
Keywords | OXIDOREDUCTASE / OXYGENASE / CYTOCHROME P450 / MONOOXYGENASE / ELECTRON TRANSPORT | ||||||
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: 1.8 Å | ||||||
Authors | Schlichting, I. / Jung, C. / Schulze, H. | ||||||
Citation | Journal: FEBS Lett. / Year: 1997 Title: Crystal structure of cytochrome P-450cam complexed with the (1S)-camphor enantiomer. Authors: Schlichting, I. / Jung, C. / Schulze, H. #1: Journal: J.Mol.Biol. / Year: 1987 Title: High-Resolution Crystal Structure of Cytochrome P450Cam Authors: Poulos, T.L. / Finzel, B.C. / Howard, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1akd.cif.gz | 100.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1akd.ent.gz | 75.7 KB | Display | PDB format |
PDBx/mmJSON format | 1akd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1akd_validation.pdf.gz | 833.5 KB | Display | wwPDB validaton report |
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Full document | 1akd_full_validation.pdf.gz | 840 KB | Display | |
Data in XML | 1akd_validation.xml.gz | 19.9 KB | Display | |
Data in CIF | 1akd_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/1akd ftp://data.pdbj.org/pub/pdb/validation_reports/ak/1akd | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 46587.895 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HEME LINKED BY CYS 357, SUBSTRATE (1S)-CAMPHOR BOUND IN TWO CONFORMATIONS, A AND B Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P00183, camphor 5-monooxygenase |
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#2: Chemical | ChemComp-K / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CAM / |
#5: 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: 2.44 Å3/Da / Density % sol: 49.55 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: dialysis / pH: 7.4 Details: PROTEIN WAS CRYSTALLIZED BY DIALYSIS FROM 10% PEG 8000, 50 MM TRISHCL PH 7.4, 250 MM KCL, 100 MM DTE, IN THE PRESENCE OF EXCESS (1S)-CAMPHOR., dialysis | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jan 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→26 Å / Num. obs: 41095 / % possible obs: 92 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.284 / Rsym value: 0.284 / % possible all: 69.4 |
Reflection | *PLUS Num. measured all: 143928 |
Reflection shell | *PLUS % possible obs: 69.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNPUBLISHED COORDINATES FROM TETRAGONAL FORM OF P450CAM Resolution: 1.8→26 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0
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Displacement parameters | Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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