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Yorodumi- PDB-5xqa: Crystal Structure of Transketolase in complex with ribose-5-phosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xqa | |||||||||
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Title | Crystal Structure of Transketolase in complex with ribose-5-phosphate from Pichia Stipitis | |||||||||
Components | Transketolase | |||||||||
Keywords | TRANSFERASE / transketolase | |||||||||
Function / homology | Function and homology information purine nucleotide metabolic process / carbohydrate derivative metabolic process / transketolase / transketolase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Scheffersomyces stipitis CBS 6054 (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å | |||||||||
Authors | Li, T.L. / Hsu, N.S. / Wang, Y.L. | |||||||||
Citation | Journal: Chembiochem / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xqa.cif.gz | 314 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xqa.ent.gz | 245.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xqa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/5xqa ftp://data.pdbj.org/pub/pdb/validation_reports/xq/5xqa | HTTPS FTP |
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-Related structure data
Related structure data | 5xpsC 5xqkC 5xrvC 5xt0C 5xt4C 5xtxC 5xu2C 5xu9C 5hyvS 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
#1: Protein | Mass: 75054.453 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scheffersomyces stipitis CBS 6054 (fungus) Strain: CBS 6054 / Gene: TKT, TKT1, PICST_67105 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: P34736, transketolase |
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#2: Chemical | ChemComp-TPP / |
#3: Chemical | ChemComp-CA / |
#4: Sugar | ChemComp-HSX / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.07 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→30 Å / Num. obs: 305278 / % possible obs: 96.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.14→1.18 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HYV Resolution: 1.14→30 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.725 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.024 / ESU R Free: 0.024 / 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: 9.189 Å2
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Refinement step | Cycle: 1 / Resolution: 1.14→30 Å
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Refine LS restraints |
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