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Yorodumi- PDB-2ez9: Pyruvate oxidase variant F479W in complex with reaction intermedi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ez9 | ||||||
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Title | Pyruvate oxidase variant F479W in complex with reaction intermediate analogue 2-phosphonolactyl-thiamin diphosphate | ||||||
Components | Pyruvate oxidase | ||||||
Keywords | OXIDOREDUCTASE / TPP enzyme / reaction intermediate analogue | ||||||
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: 1.6 Å | ||||||
Authors | Wille, G. / Meyer, D. / Steinmetz, A. / Hinze, E. / Golbik, R. / Tittmann, K. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2006 Title: The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Authors: Wille, G. / Meyer, D. / Steinmetz, A. / Hinze, E. / Golbik, R. / Tittmann, K. | ||||||
History |
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Remark 999 | SEQUENCE Author states that residue 561 is indeed a MET. The THR from the SWS database is an error ...SEQUENCE Author states that residue 561 is indeed a MET. The THR from the SWS database is an error in the database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ez9.cif.gz | 264.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ez9.ent.gz | 208 KB | Display | PDB format |
PDBx/mmJSON format | 2ez9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/2ez9 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/2ez9 | HTTPS FTP |
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-Related structure data
Related structure data | 2ez4C 2ez8C 2eztC 2ezuC 1powS 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 on special symmetry positions |
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Details | The biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operation: x, -y+1, -z |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 66245.836 Da / Num. of mol.: 2 / Mutation: F479W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: pox5 / Plasmid: pBP200 / Production host: Escherichia coli (E. coli) / Strain (production host): C600 / References: UniProt: P37063, pyruvate oxidase |
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-Non-polymers , 5 types, 1038 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.9 Å3/Da / Density % sol: 56.8 % |
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Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 16, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.84 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→19.62 Å / Num. all: 165388 / Num. obs: 165340 / % possible obs: 83 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.7 / Redundancy: 4.6 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.089 / Χ2: 0.766 / Net I/σ(I): 12.14 |
Reflection shell | Resolution: 1.6→1.62 Å / % possible obs: 75.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.4 / Num. measured obs: 5969 / Χ2: 0.533 / % possible all: 0.759 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1POW Resolution: 1.6→19.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.161 / WRfactor Rwork: 0.142 / SU B: 1.147 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: Engh & Huber / 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 / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.157 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→19.62 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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