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Yorodumi- PDB-2vjy: Pyruvate decarboxylase from Kluyveromyces lactis in complex with ... -
+Open data
-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 | |||||||||
Components | PYRUVATE DECARBOXYLASE | |||||||||
Keywords | 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 | Function and homology information 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 | KLUYVEROMYCES LACTIS (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Kutter, S. / Wille, G. / Weiss, M.S. / Konig, S. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vjy.cif.gz | 457.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vjy.ent.gz | 371.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vjy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vjy_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2vjy_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 2vjy_validation.xml.gz | 94.1 KB | Display | |
Data in CIF | 2vjy_validation.cif.gz | 131.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/2vjy ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjy | HTTPS FTP |
-Related structure data
Related structure data | 2vk1C 2vk8C 2g1i S: Starting model for refinement C: citing same article (ref.) |
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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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-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) KLUYVEROMYCES LACTIS (yeast) / References: UniProt: Q12629, pyruvate decarboxylase |
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-Non-polymers , 5 types, 1067 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.93001 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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