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Yorodumi- PDB-2vk1: Crystal structure of the Saccharomyces cerevisiae pyruvate decarb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vk1 | |||||||||
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Title | Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant D28A in complex with its substrate | |||||||||
Components | PYRUVATE DECARBOXYLASE ISOZYME 1 | |||||||||
Keywords | LYASE / ASYMMETRIC ACTIVE SITES / PHENYLALANINE CATABOLISM / TRYPTOPHAN CATABOLISM / THIAMINE PYROPHOSPHATE / DIMER OF DIMERS / PHOSPHORYLATION / ALLOSTERIC ENZYME / TDP / TPP / NUCLEUS / PYRUVATE / CYTOPLASM / BRANCHED-CHAIN AMINO ACID CATABOLISM / SUBSTRATE ACTIVATION / THIAMINE DIPHOSPHATE / MAGNESIUM / ACETYLATION / METAL-BINDING / DECARBOXYLASE | |||||||||
Function / homology | Function and homology information phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / glycolytic fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases ...phenylpyruvate decarboxylase / branched-chain-2-oxoacid decarboxylase / phenylpyruvate decarboxylase activity / branched-chain-2-oxoacid decarboxylase activity / indolepyruvate decarboxylase / glycolytic fermentation to ethanol / indolepyruvate decarboxylase activity / aromatic amino acid family catabolic process to alcohol via Ehrlich pathway / pyruvate decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / branched-chain amino acid catabolic process / tryptophan catabolic process / L-phenylalanine catabolic process / pyruvate metabolic process / thiamine pyrophosphate binding / magnesium ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | |||||||||
Authors | Kutter, S. / Weik, M. / 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 | 2vk1.cif.gz | 463.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vk1.ent.gz | 378 KB | Display | PDB format |
PDBx/mmJSON format | 2vk1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vk/2vk1 ftp://data.pdbj.org/pub/pdb/validation_reports/vk/2vk1 | HTTPS FTP |
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-Related structure data
Related structure data | 2vjyC 2vk8C 1qpbS 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
#1: Protein | Mass: 61512.996 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PUC 18 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM 109 / References: UniProt: P06169, pyruvate decarboxylase #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PYR / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ASP 28 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 28 TO ALA ...ENGINEERED | |
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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: 2.54 Å3/Da / Density % sol: 51.59 % / Description: NONE |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 6.35 Details: 15MM CITRATE, 1,67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1MG SCPDC/ML PH 6. ...Details: 15MM CITRATE, 1,67MM MES, 315MM PYRUVATE, 1MM NADH, 0.001MG/ML ALCOHOL DEHYDROGENASE, 1.67MM TDP, 1.67MM MAGNESIUM SULFATE, 1.67MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1MG SCPDC/ML PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273.15C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→99 Å / Num. obs: 262151 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.71→1.74 Å / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QPB Resolution: 1.71→109.11 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.102 / 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: 20.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→109.11 Å
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Refine LS restraints |
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