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- PDB-2ez8: Pyruvate oxidase variant F479W in complex with reaction intermedi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ez8 | |||||||||
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Title | Pyruvate oxidase variant F479W in complex with reaction intermediate 2-lactyl-thiamin diphosphate | |||||||||
![]() | Pyruvate oxidase | |||||||||
![]() | OXIDOREDUCTASE / TPP enzyme / reaction intermediate | |||||||||
Function / homology | ![]() pyruvate oxidase / pyruvate oxidase activity / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wille, G. / Meyer, D. / Steinmetz, A. / Hinze, E. / Golbik, R. / Tittmann, K. | |||||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 264.9 KB | Display | ![]() |
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PDB format | ![]() | 208.3 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 | ![]() | 51.2 KB | Display | |
Data in CIF | ![]() | 76.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ez4C ![]() 2ez9C ![]() 2eztC ![]() 2ezuC ![]() 1powS 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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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 |
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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.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 1003 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TDL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/TDL.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 280 K / Method: hanging drop / pH: 5.7 Details: ammonium sulfate, potassium phosphate, pH 5.7, hanging drop, temperature 280K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.97→24.96 Å / Num. all: 105614 / Num. obs: 105590 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.7 / Redundancy: 4.5 % / Biso Wilson estimate: 12.8 Å2 / Rmerge(I) obs: 0.107 / Χ2: 0.899 / Net I/σ(I): 11.49 |
Reflection shell | Resolution: 1.97→2 Å / % possible obs: 87.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 3728 / Χ2: 0.859 / % possible all: 0.871 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1POW Resolution: 1.963→24.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.145 / WRfactor Rwork: 0.127 / SU B: 2.396 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.108 / 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: 13.078 Å2
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Refinement step | Cycle: LAST / Resolution: 1.963→24.96 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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