[English] 日本語
Yorodumi- PDB-2c3y: CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXID... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c3y | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE RADICAL FORM 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 / iron ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | DESULFOVIBRIO AFRICANUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2c3y.cif.gz | 524.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2c3y.ent.gz | 417.4 KB | Display | PDB format |
PDBx/mmJSON format | 2c3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/2c3y ftp://data.pdbj.org/pub/pdb/validation_reports/c3/2c3y | HTTPS FTP |
---|
-Related structure data
Related structure data | 2c3mC 2c3oC 2c3pC 2c3uC 2c42C 2uzaC 1kekS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 OVERNIGHT WITH PYRUVATE Source: (natural) DESULFOVIBRIO AFRICANUS (bacteria) / References: UniProt: P94692, pyruvate synthase |
---|
-Non-polymers , 6 types, 1992 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.42 % |
---|---|
Crystal grow | pH: 9 / Details: 10% PEG6000, 100MM MGCL2, 100MM TRIS-HCL PH 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975633 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 14, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975633 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 182457 / % possible obs: 90.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 10.3 Å2 / Rsym value: 0.1 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.93→2.1 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.27 / % possible all: 89.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1KEK Resolution: 1.93→8 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3833227.31 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 70.7952 Å2 / ksol: 0.454456 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|