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- PDB-2vk4: Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vk4 | |||||||||
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Title | Crystal structure of pyruvate decarboxylase from Kluyveromyces lactis | |||||||||
![]() | PYRUVATE DECARBOXYLASE | |||||||||
![]() | LYASE / METAL-BINDING / DECARBOXYLASE / DIMER OF DIMERS / SUBSTRATE ACTIVATION / THIAMINE DIPHOSPHATE / TDP / TPP / MAGNESIUM / FLAVOPROTEIN / THIAMINE PYROPHOSPHATE / ASYMMETRIC ACTIVE SITES | |||||||||
Function / homology | ![]() pyruvate decarboxylase / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kutter, S. / Relle, S. / Wille, G. / Weiss, M.S. / Konig, S. | |||||||||
![]() | ![]() Title: Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story. Authors: Konig, S. / Spinka, M. / Kutter, S. #1: Journal: FEBS J. / Year: 2006 Title: The Crystal Structure of Pyruvate Decarboxylase from Kluyveromyces Lactis. Implications for the Substrate Activation Mechanism of This Enzyme. Authors: Kutter, S. / Wille, G. / Relle, S. / Weiss, M.S. / Hubner, G. / Konig, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 458.6 KB | Display | ![]() |
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PDB format | ![]() | 372.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 93.9 KB | Display | |
Data in CIF | ![]() | 134.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2w93C ![]() 2g1i 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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Components
#1: Protein | Mass: 61716.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.59 % / Description: NONE |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.45 Details: 50MM MES, 1MM DTT, 5MM TDP, 5MM MAGNESIUM SULFATE, 10% PEG 2000, 10% PEG 8000, 2MG KLPDC/ML, PH 6.45, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 281K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8125 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.45 Å / Num. obs: 155315 / % possible obs: 86.3 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.95→2.06 Å / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.5 / % possible all: 80.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G1I ![]() 2g1i Resolution: 1.95→48.45 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.163 / 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: 22.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.45 Å
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Refine LS restraints |
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