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Yorodumi- PDB-6efh: Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6efh | ||||||
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Title | Pyruvate decarboxylase from Kluyveromyces lactis soaked with pyruvamide | ||||||
Components | Pyruvate decarboxylase | ||||||
Keywords | LYASE / pyruvate decarboxylase / thiamine diphosphate / substrate activation / pyruvamide | ||||||
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: 2.99 Å | ||||||
Authors | Kutter, S. / Konig, S. | ||||||
Citation | Journal: To be Published Title: The crystal structures of pyruvate decarboxylase from Kluyveromyces lactis in the absence of ligands and in the presence of the substrate surrogate pyruvamide Authors: Kutter, S. / Konig, S. #1: 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 | 6efh.cif.gz | 225.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6efh.ent.gz | 181.2 KB | Display | PDB format |
PDBx/mmJSON format | 6efh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6efh_validation.pdf.gz | 982.5 KB | Display | wwPDB validaton report |
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Full document | 6efh_full_validation.pdf.gz | 999.9 KB | Display | |
Data in XML | 6efh_validation.xml.gz | 40.7 KB | Display | |
Data in CIF | 6efh_validation.cif.gz | 55.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/6efh ftp://data.pdbj.org/pub/pdb/validation_reports/ef/6efh | HTTPS FTP |
-Related structure data
Related structure data | 6efgC 2vk4S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 61716.762 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast) Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q12629, pyruvate decarboxylase |
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-Non-polymers , 5 types, 48 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-1PE / | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 3.22 Å3/Da / Density % sol: 61.8 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, ...Details: 2 mg/mL KlPDC in 2 mM MES, 18 mM citrate, pH 6.25, 4 mM thiamine diphosphate, 4 mM magnesium sulfate, 2 mM DTT, 1:1 with mother liquor (18-24% w/v PEG2000/PEG6000), ~25 days at 8 degrees C, soaked for 50 seconds in 2 uL mother liquor + 2 uL 90% v/v PEG400, 200 mM pyruvamide prior to flash freezing |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 7, 2007 |
Radiation | Monochromator: Diamond (001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→55.6 Å / Num. obs: 32279 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 25.68 Å2 / Rmerge(I) obs: 0.333 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.99→3.05 Å / Redundancy: 14.7 % / Rmerge(I) obs: 1.797 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1591 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2VK4 Resolution: 2.99→55.6 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.846 / SU B: 20.033 / SU ML: 0.351 / Cross valid method: THROUGHOUT / ESU R Free: 0.423 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→55.6 Å
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Refine LS restraints |
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