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Yorodumi- PDB-1w85: The crystal structure of pyruvate dehydrogenase E1 bound to the p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w85 | ||||||||||||
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Title | The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2 | ||||||||||||
Components |
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Keywords | OXIDOREDUCTASE / PYRUVATE / DEHYDROGENASE / DIHYDROLIPOYL / ACETYL TRANSFERASE / MULTIENZYME COMPLEX / TRANSFERASE | ||||||||||||
Function / homology | Function and homology information pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / lipoic acid binding / branched-chain amino acid catabolic process / cytoplasm Similarity search - Function | ||||||||||||
Biological species | GEOBACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / Perham, R.N. / Luisi, B.F. | ||||||||||||
Citation | Journal: Science / Year: 2004 Title: A molecular switch and proton wire synchronize the active sites in thiamine enzymes. Authors: Frank, R.A. / Titman, C.M. / Pratap, J.V. / Luisi, B.F. / Perham, R.N. #1: Journal: To be Published Title: Molecular Assembly of a Multi-Enzymes Complex: The Crystal Structure of Pyruvate Dehydrogenase E1 Bound to the Peripheral Subunit Binding Domain of E2 Authors: Frank, R.A.W. / Pratap, J.V. / Pei, X.Y. / 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 | 1w85.cif.gz | 572.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w85.ent.gz | 465.9 KB | Display | PDB format |
PDBx/mmJSON format | 1w85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w85_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1w85_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1w85_validation.xml.gz | 116.4 KB | Display | |
Data in CIF | 1w85_validation.cif.gz | 166.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w85 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w85 | HTTPS FTP |
-Related structure data
Related structure data | 1w88C 1qs0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.975356, -0.219264, -0.024566), Vector: Details | FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350FOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350 | |
-Components
-PYRUVATE DEHYDROGENASE E1 COMPONENT, ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 41386.980 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P21873, pyruvate dehydrogenase (acetyl-transferring) #2: Protein | Mass: 35364.441 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P21874, pyruvate dehydrogenase (acetyl-transferring) |
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-Protein/peptide , 1 types, 2 molecules IJ
#3: Protein/peptide | Mass: 5262.105 Da / Num. of mol.: 2 Fragment: PERIPHERAL SUBUNIT BINDING DOMAIN (PSBD), RESIDUES 122-170 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase |
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-Non-polymers , 5 types, 1750 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Chemical | ChemComp-TPP / #7: Chemical | ChemComp-K / #8: 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: 2.21 Å3/Da / Density % sol: 44.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 10% PEG 5500 MONOMETHYL ETHER, 0.2M IMIDAZOLE MALATE PH5. 20DEG C, SITTING-DROP., pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.95 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 20, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 171898 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.7 / % possible all: 68.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QS0 Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: THE FOLLOWING TERMINAL RESIDUES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY MAP AND ARE NOT MODELLED: A1-A3, A368, C1-C3, E1-E4, G1-G4, I122-I127, I170, J122-J128, J167-J170. IN ...Details: THE FOLLOWING TERMINAL RESIDUES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY MAP AND ARE NOT MODELLED: A1-A3, A368, C1-C3, E1-E4, G1-G4, I122-I127, I170, J122-J128, J167-J170. IN ADDITION, THE FOLLOWING RESIDUES COULD NOT BE MODELLED: A277-A282, E204-E211, E278- E283, J147-J150.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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