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- PDB-3duf: Snapshots of catalysis in the E1 subunit of the pyruvate dehydrog... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3duf | ||||||
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Title | Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex | ||||||
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![]() | OXIDOREDUCTASE/TRANSFERASE / OXIDOREDUCTASE / PYRUVATE / DEHYDROGENASE / DIHYDROLIPOYL / ACETYL TRANSFERASE / MULTIENZYME COMPLEX / TRANSFERASE / Glycolysis / Phosphoprotein / Thiamine pyrophosphate / Acyltransferase / OXIDOREDUCTASE-TRANSFERASE COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pei, X.Y. / Titman, C.M. / Frank, R.A.W. / Leeper, F.J. / Luisi, B.F. | ||||||
![]() | ![]() Title: Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex Authors: Pei, X.Y. / Titman, C.M. / Frank, R.A. / Leeper, F.J. / Luisi, B.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 570.3 KB | Display | ![]() |
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PDB format | ![]() | 454.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 103.1 KB | Display | |
Data in CIF | ![]() | 140.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dv0C ![]() 3dvaC ![]() 1w85S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 6
NCS ensembles :
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Components
-Pyruvate dehydrogenase E1 component subunit ... , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 41518.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P21873, pyruvate dehydrogenase (acetyl-transferring) #2: Protein | Mass: 35495.633 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P21874, pyruvate dehydrogenase (acetyl-transferring) |
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-Protein , 1 types, 2 molecules IJ
#3: Protein | Mass: 46392.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P11961, dihydrolipoyllysine-residue acetyltransferase |
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-Non-polymers , 4 types, 418 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/R1T.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/R1T.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-R1T / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.72 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the ...Details: The protein solution was then mixed in 1:1 volume ratio of crystallization buffer consisting of 8-12 % mono-methyl ether polyethylene glycol (MME PEG) 5000, 0.1 M Na maleate pH 5.5, and the droplet was left to equilibrate against a reservoir of neat crystallization buffer., VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 11, 2005 / Details: mirror |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→66 Å / Num. all: 99540 / Num. obs: 99351 / % possible obs: 98.9 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 3.7 % / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.302 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1W85 Resolution: 2.5→59.44 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.888 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.087 / ESU R Free: 0.328 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.879 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→59.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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