+Open data
-Basic information
Entry | Database: PDB / ID: 2jgd | ||||||
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Title | E. COLI 2-oxoglutarate dehydrogenase (E1o) | ||||||
Components | (2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT) x 2 | ||||||
Keywords | OXIDOREDUCTASE / 2-OXOGLUTARATE DEHYDROGENASE / FLAVOPROTEIN / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / ADENOSINE MONOPHOSPHATE / E1O / KGDH / OGDH / GLYCOLYSIS / OXALOACETATE | ||||||
Function / homology | Function and homology information oxoglutarate dehydrogenase (succinyl-transferring) / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / thiamine pyrophosphate binding / tricarboxylic acid cycle / nucleotide binding / magnesium ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Frank, R.A.W. / Price, A.J. / Northrop, F.D. / Perham, R.N. / Luisi, B.F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of the E1 Component of the Escherichia Coli 2-Oxoglutarate Dehydrogenase Multienzyme Complex. Authors: Frank, R.A.W. / Price, A.J. / Northrop, F.D. / Perham, R.N. / Luisi, B.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jgd.cif.gz | 342.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jgd.ent.gz | 281.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jgd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jgd ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jgd | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.79032, 0.61229, -0.02206), Vector: |
-Components
#1: Protein | Mass: 105170.680 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0AFG3, oxoglutarate dehydrogenase (succinyl-transferring) | ||
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#2: Protein | Mass: 105209.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0AFG3, oxoglutarate dehydrogenase (succinyl-transferring) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.67 % Description: SELENIUM SITES WERE FOUND WITH MAD DATA IN SHELXD. PHASES WERE DETERMINED WITH SAD DATA IN PHASER |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.6 Details: SITTING DROP: 1UL 12% PEG 4000, 50MM SOCIUM CITRATE PH5.6. 1UL 10MG/ML TE1O. RESERVOIR: 1UL 12% PEG 4000, 50MM SOCIUM CITRATE PH5.6., pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939272 |
Detector | Detector: CCD / Date: May 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939272 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→70 Å / Num. obs: 80455 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→29.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.276 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→29.09 Å
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