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- PDB-5gxg: High-resolution crystal structure of the electron transfer comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gxg | ||||||
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Title | High-resolution 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. / Ubbink, M. / Nojiri, M. | ||||||
![]() | ![]() Title: Identification of productive and futile encounters in an electron transfer protein complex Authors: Andraojc, W. / Hiruma, Y. / Liu, W.M. / Ravera, E. / Nojiri, M. / Parigi, G. / Luchinat, C. / Ubbink, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.3 KB | Display | ![]() |
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PDB format | ![]() | 93.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 842.1 KB | Display | ![]() |
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Full document | ![]() | 850.8 KB | Display | |
Data in XML | ![]() | 24.5 KB | Display | |
Data in CIF | ![]() | 35.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3w9cS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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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: 11617.159 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 302 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DTT.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-DTT / | #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: 39.28 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES, 0.1M Sodium Chloride, 1.6M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→61.66 Å / Num. obs: 51169 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 39.2 |
Reflection shell | Resolution: 1.7→1.73 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3w9c Resolution: 1.7→59.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.024 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.446 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→59.66 Å
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Refine LS restraints |
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