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- PDB-2vjy: Pyruvate decarboxylase from Kluyveromyces lactis in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vjy | |||||||||
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Title | Pyruvate decarboxylase from Kluyveromyces lactis in complex with the substrate analogue methyl acetylphosphonate | |||||||||
![]() | PYRUVATE DECARBOXYLASE | |||||||||
![]() | LYASE / METAL-BINDING / DECARBOXYLASE / DIMER OF DIMERS / METHYLACETYLPHOSPHONATE / METHYL ACETYLPHOSPHONATE / SUBSTRATE ACTIVATION / THIAMINE DIPHOSPHATE / THIAMINE PYROPHOSPHATE / ASYMMETRIC ACTIVE SITES / MAP / PYRUVATE / MAGNESIUM / FLAVOPROTEIN | |||||||||
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. / Wille, G. / Weiss, M.S. / Konig, S. | |||||||||
![]() | ![]() Title: Covalently Bound Substrate at the Regulatory Site of Yeast Pyruvate Decarboxylases Triggers Allosteric Enzyme Activation. Authors: Kutter, S. / Weiss, M.S. / Wille, G. / Golbik, R. / Spinka, M. / 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 | ![]() | 457.6 KB | Display | ![]() |
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PDB format | ![]() | 371.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 94.1 KB | Display | |
Data in CIF | ![]() | 131.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vk1C ![]() 2vk8C ![]() 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 61716.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 1067 molecules ![](data/chem/img/TPP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALK.gif)
![](data/chem/img/ALU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ALK.gif)
![](data/chem/img/ALU.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ALK / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.68 % / Description: NONE |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 20MM CITRATE, 10% PEG2000, 10% PEG6000, 5MM TDP, 5MM MAGNESIUM SULFATE, 1MM DTT, 40MM METHYL ACETYLPHOSPHONATE, PH 6.1, 0.95MG KLPDC/ML, 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: Dec 6, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93001 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→99 Å / Num. obs: 100426 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2G1I ![]() 2g1i Resolution: 2.3→20.19 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.306 / ESU R Free: 0.225 / 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: 26.26 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20.19 Å
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Refine LS restraints |
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