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Yorodumi- PDB-3w9c: Crystal structure of the electron transfer complex of cytochrome ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3w9c | ||||||
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Title | Crystal structure of the electron transfer complex of cytochrome p450cam with putidaredoxin | ||||||
Components |
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Keywords | OXIDOREDUCTASE/ELECTRON TRANSPORT / inter-protein electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | Function and homology information P450-containing electron transport chain / camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding / heme binding ...P450-containing electron transport chain / camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding / heme binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kikui, Y. / Hiruma, Y. / Hass, M.A. / Koteishi, H. / Ubbink, M. / Nojiri, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: The structure of the cytochrome p450cam-putidaredoxin complex determined by paramagnetic NMR spectroscopy and crystallography. Authors: Hiruma, Y. / Hass, M.A. / Kikui, Y. / Liu, W.M. / Olmez, B. / Skinner, S.P. / Blok, A. / Kloosterman, A. / Koteishi, H. / Lohr, F. / Schwalbe, H. / Nojiri, M. / Ubbink, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3w9c.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3w9c.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 3w9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/3w9c ftp://data.pdbj.org/pub/pdb/validation_reports/w9/3w9c | HTTPS FTP |
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-Related structure data
Related structure data | 2m56C 1oqrS 2zwuS 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 46664.973 Da / Num. of mol.: 1 / Mutation: K126C, R130C, C334A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase |
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#2: Protein | Mass: 11601.094 Da / Num. of mol.: 1 / Mutation: C73S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00259 |
-Non-polymers , 5 types, 42 molecules
#3: Chemical | ChemComp-HEM / | ||||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-FES / | #7: 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: 2.03 Å3/Da / Density % sol: 39.5 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES (PH7.5), 0.1M SODIUM CHLORIDE, 1.6M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-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 MX225HE / Detector: CCD / Date: Feb 3, 2012 |
Radiation | Monochromator: DOUBLE CRYSTAL SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→61.78 Å / Num. obs: 16251 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.44 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZWU, 1OQR Resolution: 2.5→61.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.585 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 31.689 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→61.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.501→2.566 Å / Total num. of bins used: 20
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