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- PDB-5xu9: Crystal Structure of Transketolase in complex with TPP intermedia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xu9 | ||||||
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Title | Crystal Structure of Transketolase in complex with TPP intermediate IX and gauche form erythrose-4-phosphate from Pichia Stipitis | ||||||
![]() | Transketolase | ||||||
![]() | TRANSFERASE / transketolase | ||||||
Function / homology | ![]() transketolase / transketolase activity / pentose-phosphate shunt / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T.L. / Hsu, N.S. / Wang, Y.L. | ||||||
![]() | ![]() Title: Evidence of Diradicals Involved in the Yeast Transketolase Catalyzed Keto-Transferring Reactions. Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Ke, S.C. / Lyu, S.Y. / Hsu, L.J. / Li, Y.S. / Chen, S.C. / Wang, K.C. / Li, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.1 KB | Display | ![]() |
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PDB format | ![]() | 228.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xpsC ![]() 5xqaC ![]() 5xqkC ![]() 5xrvC ![]() 5xt0C ![]() 5xt4C ![]() 5xtxC ![]() 5xu2C ![]() 5hyvS 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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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/E4P.gif)
![](data/chem/img/E4P.gif)
#1: Protein | Mass: 75054.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Production host: ![]() ![]() |
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#5: Sugar | ChemComp-E4P / |
-Non-polymers , 4 types, 744 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/8N9.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/8N9.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||
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#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-8N9 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M MES, 0.1M NaCl, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: May 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→30 Å / Num. obs: 307358 / % possible obs: 95.3 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.16→1.2 Å / Rmerge(I) obs: 0.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HYV Resolution: 1.166→19.61 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.54
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.166→19.61 Å
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Refine LS restraints |
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LS refinement shell |
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