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Yorodumi- PDB-2w93: Crystal structure of the Saccharomyces cerevisiae pyruvate decarb... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w93 | ||||||
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Title | Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide | ||||||
Components | PYRUVATE DECARBOXYLASE ISOZYME 1 | ||||||
Keywords | LYASE / SUBSTRATE ACTIVATION / SUBSTRATE REGULATION / NUCLEUS / CYTOPLASM / MAGNESIUM / ACETYLATION / PHOSPHOPROTEIN / ALLOSTERIC ENZYME / THIAMINE PYROPHOSPHATE / PHENYLALANINE CATABOLISM / TRYPTOPHAN CATABOLISM / PYRUVATE DECARBOXYLASE / BRANCHED-CHAIN AMINO ACID CATABOLISM / METAL-BINDING / THIOHEMIKETAL / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kutter, S. / Weiss, M.S. / Konig, S. | ||||||
Citation | Journal: J.Mol.Catal., B Enzym. / Year: 2014 Title: Allosteric Activation of Pyruvate Decarboxylases. A Never-Ending Story. Authors: Konig, S. / Spinka, M. / Kutter, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w93.cif.gz | 459.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w93.ent.gz | 371.3 KB | Display | PDB format |
PDBx/mmJSON format | 2w93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w93_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2w93_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2w93_validation.xml.gz | 91.9 KB | Display | |
Data in CIF | 2w93_validation.cif.gz | 134.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w9/2w93 ftp://data.pdbj.org/pub/pdb/validation_reports/w9/2w93 | HTTPS FTP |
-Related structure data
Related structure data | 2vk4C 2vk8S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61571.035 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): JM109 / References: UniProt: P06169, pyruvate decarboxylase #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PY0 / ( #5: 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: 2.21 Å3/Da / Density % sol: 44.41 % / Description: NONE |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.35 Details: 15 MM CITRATE, 1.67 MM MES, 300 MM PYRUVAMIDE, 1.67 MM TDP, 1.67 MM MAGNESIUM SUFATE, 1.67 MM DTT, 11.25% PEG 2000, 11.25% PEG 6000, 1.1 MG SCPDC/ML, PH 6.35, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE, 281 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→99 Å / Num. obs: 260585 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 91.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VK8 Resolution: 1.6→103.7 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.093 / 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: 24.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→103.7 Å
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Refine LS restraints |
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