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- PDB-2g25: E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2g25 | ||||||
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Title | E. Coli Pyruvate Dehydrogenase Phosphonolactylthiamin Diphosphate Complex | ||||||
![]() | Pyruvate dehydrogenase E1 component | ||||||
![]() | OXIDOREDUCTASE / PLTHDP / PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE / PYRUVATE DEHYDROGENASE E1 COMPONENT | ||||||
Function / homology | ![]() : / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / molecular adaptor activity / magnesium ion binding ...: / pyruvate dehydrogenase activity / pyruvate dehydrogenase (acetyl-transferring) / pyruvate dehydrogenase (acetyl-transferring) activity / pyruvate catabolic process / pyruvate dehydrogenase complex / thiamine pyrophosphate binding / small molecule binding / molecular adaptor activity / magnesium ion binding / protein homodimerization activity / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Furey, W. / Arjunan, P. / Chandrasekhar, K. | ||||||
![]() | ![]() Title: A Thiamin-bound, Pre-decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals ...Title: A Thiamin-bound, Pre-decarboxylation Reaction Intermediate Analogue in the Pyruvate Dehydrogenase E1 Subunit Induces Large Scale Disorder-to-Order Transformations in the Enzyme and Reveals Novel Structural Features in the Covalently Bound Adduct. Authors: Arjunan, P. / Sax, M. / Brunskill, A. / Chandrasekhar, K. / Nemeria, N. / Zhang, S. / Jordan, F. / Furey, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 347.8 KB | Display | ![]() |
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PDB format | ![]() | 276.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 64.2 KB | Display | |
Data in CIF | ![]() | 91 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2g28C ![]() 1l8aS 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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Unit cell |
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Components
#1: Protein | Mass: 99657.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AFG8, pyruvate dehydrogenase (acetyl-transferring) #2: Chemical | #3: Chemical | ChemComp-PO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG2000 MONOMETHYL ETHER, PROPANOL, SODIUM AZIDE, HEPES BUFFER, MAGNESIUM CHLORIDE, PHOSPHONOLACTYL- THIAMIN DIPHOSPHATE, PH 7.00, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Mar 25, 2002 / Details: Osmic Mirrors |
Radiation | Monochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.5 Å / Num. all: 99699 / Num. obs: 99699 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.087 / Net I/σ(I): 24.82 |
Reflection shell | Resolution: 2.1→2.19 Å / Mean I/σ(I) obs: 5.51 / % possible all: 60 |
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Processing
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 1L8A Resolution: 2.1→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 10.55 Å2 | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 7
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