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- PDB-3w9c: Crystal structure of the electron transfer complex of cytochrome ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3w9c | ||||||
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Title | Crystal structure of the electron transfer complex of cytochrome p450cam with putidaredoxin | ||||||
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![]() | OXIDOREDUCTASE/ELECTRON TRANSPORT / inter-protein electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT complex | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kikui, Y. / Hiruma, Y. / Hass, M.A. / Koteishi, H. / Ubbink, M. / Nojiri, M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 87.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.5 KB | Display | ![]() |
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Full document | ![]() | 800.7 KB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2m56C ![]() 1oqrS ![]() 2zwuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 42 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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