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- PDB-5xqk: Crystal Structure of Transketolase in complex with xylulose-5-pho... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xqk | ||||||
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Title | Crystal Structure of Transketolase in complex with xylulose-5-phosphate from Pichia Stipitis | ||||||
![]() | Transketolase![]() | ||||||
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Function / homology | ![]() purine nucleotide metabolic process / carbohydrate derivative metabolic process / ![]() ![]() ![]() 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 | ![]() | 304.3 KB | Display | ![]() |
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PDB format | ![]() | 241.5 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 ![]() 5xrvC ![]() 5xt0C ![]() 5xt4C ![]() 5xtxC ![]() 5xu2C ![]() 5xu9C ![]() 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
#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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#2: Chemical | ChemComp-T5X / | ||
#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-PEG / ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.05 Å3/Da / Density % sol: 59.62 % |
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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: Sep 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.12→30 Å / Num. obs: 312132 / % possible obs: 99.6 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5HYV Resolution: 1.12→30 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.635 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.951 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→30 Å
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Refine LS restraints |
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