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Open data
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Basic information
Entry | Database: PDB / ID: 6efg | ||||||
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Title | Pyruvate decarboxylase from Kluyveromyces lactis | ||||||
![]() | Pyruvate decarboxylase | ||||||
![]() | LYASE / pyruvate decarboxylase / thiamine diphosphate / substrate activation | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kutter, S. / Konig, S. | ||||||
![]() | ![]() 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: ![]() Title: The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme. Authors: Kutter, S. / Wille, G. / Relle, S. / Weiss, M.S. / Hubner, G. / Konig, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 421.3 KB | Display | ![]() |
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PDB format | ![]() | 342 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 76.8 KB | Display | |
Data in CIF | ![]() | 105.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6efhC ![]() 2vk4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61716.762 Da / Num. of mol.: 4 / Source method: isolated from a natural source Source: (natural) ![]() Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37 References: UniProt: Q12629, pyruvate decarboxylase #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48 % |
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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 30 seconds in 2 uL mother liquor + 2 uL 15% w/v glycerol, 200 mM acetaldehyde prior to flash freezing. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 21, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→38.25 Å / Num. obs: 126964 / % possible obs: 93.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 24.75 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.065 / Rrim(I) all: 0.109 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.04→2.08 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4511 / CC1/2: 0.689 / Rpim(I) all: 0.508 / Rrim(I) all: 0.837 / % possible all: 66.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2VK4 Resolution: 2.04→38.25 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.157 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.223 / 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: 37.997 Å2
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Refinement step | Cycle: 1 / Resolution: 2.04→38.25 Å
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Refine LS restraints |
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