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Yorodumi- PDB-2c42: Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c42 | |||||||||
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Title | Crystal Structure Of Pyruvate-Ferredoxin Oxidoreductase From Desulfovibrio africanus | |||||||||
Components | PYRUVATE-FERREDOXIN OXIDOREDUCTASEPyruvate synthase | |||||||||
Keywords | OXIDOREDUCTASE / 4FE-4S / IRON / IRON-SULFUR / IRON-SULFUR CLUSTER / PYRUVATE CATABOLISM / TPP-DEPENDENT ENZYME / METAL-BINDING / ELECTRON TRANSPORT | |||||||||
Function / homology | Function and homology information 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 | DESULFOVIBRIO AFRICANUS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | |||||||||
Authors | Cavazza, C. / Contreras-Martel, C. / Pieulle, L. / Chabriere, E. / Hatchikian, E.C. / Fontecilla-Camps, J.C. | |||||||||
Citation | Journal: Structure / Year: 2006 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: Journal: Science / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c42.cif.gz | 505.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c42.ent.gz | 404.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c42.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c42 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c42 | HTTPS FTP |
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-Related structure data
Related structure data | 2c3mC 2c3oC 2c3pC 2c3uC 2c3yC 2uzaC 1kekS 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 , 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, SOAKING 16 MIN. WITH PYRUVIC ACID (PH 6.0 AND DTT) Source: (natural) DESULFOVIBRIO AFRICANUS (bacteria) / References: UniProt: P94692, pyruvate synthase |
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-Non-polymers , 6 types, 1231 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 47.66 % |
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Crystal grow | pH: 6 Details: 10% PEG6000, 100MM MGCL2, 100MM NA CACODYLATE, 5% DTT, pH 6.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 5, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→55 Å / Num. obs: 233941 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 4.42 % / Biso Wilson estimate: 17.2 Å2 / Rsym value: 0.06 / Net I/σ(I): 16.54 |
Reflection shell | Resolution: 1.78→1.89 Å / Redundancy: 3.46 % / Mean I/σ(I) obs: 5.02 / Rsym value: 0.29 / % possible all: 75.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KEK Resolution: 1.78→51.15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4472383.33 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.9842 Å2 / ksol: 0.372721 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→51.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.89 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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