+Open data
-Basic information
Entry | Database: PDB / ID: 5euj | ||||||
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Title | PYRUVATE DECARBOXYLASE FROM ZYMOBACTER PALMAE | ||||||
Components | Pyruvate decarboxylase | ||||||
Keywords | LYASE / PYRUVATE DECARBOXYLASE | ||||||
Function / homology | Function and homology information pyruvate decarboxylase / pyruvate decarboxylase activity / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Zymobacter palmae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Buddrus, L. / Crennell, S.J. / Leak, D.J. / Danson, M.J. / Andrews, E.S.V. / Arcus, V.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal structure of pyruvate decarboxylase from Zymobacter palmae. Authors: Buddrus, L. / Andrews, E.S. / Leak, D.J. / Danson, M.J. / Arcus, V.L. / Crennell, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5euj.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5euj.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5euj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/5euj ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5euj | HTTPS FTP |
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-Related structure data
Related structure data | 2vbiS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 61875.680 Da / Num. of mol.: 24 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymobacter palmae (bacteria) / Gene: pdc / Plasmid: PET28A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8KTX6, pyruvate decarboxylase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-TPP / #4: Chemical | ChemComp-EDO / #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: 2.76 Å3/Da / Density % sol: 55.44 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.15 M SODIUM CITRATE, PH 5.5, 14% PEG 3350, 1 MM PYRUVATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2015 / Details: FOCUSSING MIRRORS (TWO |
Radiation | Monochromator: SI111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→75.47 Å / Num. obs: 858032 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / Rejects: 0 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2VBI Resolution: 2.15→75.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.501 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
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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 max: 104.19 Å2 / Biso mean: 26.635 Å2 / Biso min: 5.8 Å2
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Refinement step | Cycle: final / Resolution: 2.15→75.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.207 Å / Total num. of bins used: 20
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