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- PDB-2c3p: CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c3p | ||||||
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Title | CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM Desulfovibrio africanus | ||||||
![]() | PYRUVATE-FERREDOXIN OXIDOREDUCTASE | ||||||
![]() | OXIDOREDUCTASE / 4FE-4S / IRON / IRON-SULFUR / IRON-SULFUR CLUSTER / PYRUVATE CATABOLISM / TPP-DEPENDENT ENZYME / METAL-BINDING / ELECTRON TRANSPORT | ||||||
Function / homology | ![]() pyruvate synthase / pyruvate synthase activity / thiamine pyrophosphate binding / electron transport chain / 4 iron, 4 sulfur cluster binding / response to oxidative stress / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cavazza, C. / Contreras-Martel, C. / Pieulle, L. / Chabriere, E. / Hatchikian, E.C. / Fontecilla-Camps, J.C. | ||||||
![]() | ![]() Title: Flexibility of Thiamine Diphosphate Revealed by Kinetic Crystallographic Studies of the Reaction of Pyruvate-Ferredoxin Oxidoreductase with Pyruvate. Authors: Cavazza, C. / Contreras-Martel, C. / Pieulle, L. / Chabriere, E. / Hatchikian, E.C. / Fontecilla-Camps, J.C. #1: ![]() Title: Crystal Structure of the Free Radical Intermediate of Pyruvate:Ferredoxin Oxidoreductase. Authors: Chabriere, E. / Vernede, X. / Guigliarelli, B. / Charon, M.-H. / Hatchikian, E.C. / Fontecilla-Camps, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 499.1 KB | Display | ![]() |
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PDB format | ![]() | 398.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 94.7 KB | Display | |
Data in CIF | ![]() | 134.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c3mC ![]() 2c3oC ![]() 2c3uC ![]() 2c3yC ![]() 2c42C ![]() 2uzaC ![]() 1kekS 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 , 1 types, 2 molecules AB
#1: Protein | Mass: 133703.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: COMPLEXED WITH IRON/SULFUR CLUSTER, THIAMIN DIPHOSPHATE, CRYSTAL SOAKED 40 MINUTES WITH PYRUVATE Source: (natural) ![]() |
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-Non-polymers , 5 types, 863 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/1TP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1TP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 48.37 % |
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Crystal grow | pH: 6 / Details: 10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE PH 6 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979273 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→50 Å / Num. obs: 524442 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 11.73 |
Reflection shell | Resolution: 2.33→2.49 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.03 / Mean I/σ(I) obs: 5.37 / % possible all: 95.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1KEK Resolution: 2.33→47.37 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5206462.79 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.4579 Å2 / ksol: 0.379681 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.33→47.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.48 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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