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Yorodumi- PDB-1qpb: PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qpb | |||||||||
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Title | PYRUVATE DECARBOYXLASE FROM YEAST (FORM B) COMPLEXED WITH PYRUVAMIDE | |||||||||
Components | PYRUVATE DECARBOXYLASE (FORM B) | |||||||||
Keywords | LYASE / THIAMINE PYRUVATE / PYRUVAMIDE | |||||||||
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 PASTORIANUS (lager yeast) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Lu, G. / Dobritzsch, D. / Schneider, G. | |||||||||
Citation | Journal: Eur.J.Biochem. / Year: 2000 Title: The Structural Basis of Substrate Activation in Yeast Pyruvate Decarboxylase a Crystallographic and Kinetic Study Authors: Lu, G. / Dobritzsch, D. / Baumann, S. / Schneider, G. / Konig, S. #1: Journal: FEBS Lett. / Year: 1997 Title: Novel Tetramer Assembly of Pyruvate Decarboxylase from Brewer'S Yeast Observed in a New Crystal Form Authors: Lu, G. / Dobritzsch, D. / Konig, S. / Schneider, G. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: DSSP | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qpb.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qpb.ent.gz | 180.5 KB | Display | PDB format |
PDBx/mmJSON format | 1qpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qpb_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1qpb_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1qpb_validation.xml.gz | 45.1 KB | Display | |
Data in CIF | 1qpb_validation.cif.gz | 61.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/1qpb ftp://data.pdbj.org/pub/pdb/validation_reports/qp/1qpb | HTTPS FTP |
-Related structure data
Related structure data | 1pvdS S: Starting model for refinement |
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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: 61555.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FORM B / Source: (natural) SACCHAROMYCES PASTORIANUS (lager yeast) / Strain: WEIHENSTEPHAN 34/70 (2124, BOHEMIAN LAGER) / References: UniProt: P06169, pyruvate decarboxylase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: 8-14% PEG6000 20MM SODIUM CITRATE AT PH 5.7 1MM DTE, 5MM THDP, 5MM MGSO4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 2, 1997 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→15 Å / Num. obs: 42140 / % possible obs: 88.9 % / Observed criterion σ(I): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 33.0519 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.091 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5 / Rsym value: 0.38 / % possible all: 60 |
Reflection shell | *PLUS % possible obs: 56 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PVD Resolution: 2.4→15 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 15 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT CORRECTION WAS APPLIED.
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Displacement parameters | Biso mean: 31.0519 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati sigma a obs: 0.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.38→2.42 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 20
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Software | *PLUS Name: CNS / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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