+Open data
-Basic information
Entry | Database: PDB / ID: 1y9d | ||||||
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Title | Pyruvate Oxidase variant V265A from Lactobacillus plantarum | ||||||
Components | Pyruvate oxidase | ||||||
Keywords | OXIDOREDUCTASE / Pyruvate oxidase | ||||||
Function / homology | Function and homology information pyruvate oxidase / pyruvate oxidase activity / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Lactobacillus plantarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Wille, G. / Ritter, M. / Weiss, M.S. / Konig, S. / Mantele, W. / Hubner, G. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: The role of Val-265 for Flavin Adenine Dinulceotide (FAD) binding in pyruvate oxidase: FTIR, kinetic and crystallographic studies on the enzyme variant V265A Authors: Wille, G. / Ritter, M. / Weiss, M.S. / Konig, S. / Mantele, W. / Hubner, G. #1: Journal: Biochemistry / Year: 2003 Title: Redox-Triggered FTIR Difference Spectra of FAD in Aqueous Solution and Bound to Flavoproteins Authors: Wille, G. / Ritter, M. / Friedemann, R. / Mantele, W. / Hubner, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y9d.cif.gz | 488.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y9d.ent.gz | 392 KB | Display | PDB format |
PDBx/mmJSON format | 1y9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/1y9d ftp://data.pdbj.org/pub/pdb/validation_reports/y9/1y9d | HTTPS FTP |
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-Related structure data
Related structure data | 1powS 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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Unit cell |
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Details | The asymmetric unit in the crystal structure is identical with the native homotetramer of the enzyme. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 66178.742 Da / Num. of mol.: 4 / Mutation: V265A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: pox5 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P37063, pyruvate oxidase |
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-Non-polymers , 6 types, 1866 molecules
#2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-TPP / #6: Chemical | ChemComp-FAD / #7: 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: 2.8 Å3/Da / Density % sol: 56.11 % |
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 8, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.3 Å / Num. obs: 147394 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1POW Resolution: 2.2→27.3 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.838 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.443 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→27.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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