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Yorodumi- PDB-5xtl: Crystal Structure of Transketolase in complex with aminopyrimidin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xtl | ||||||
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Title | Crystal Structure of Transketolase in complex with aminopyrimidine and cysteine sulfonic acid adduct from Pichia Stipitis | ||||||
Components | Transketolase | ||||||
Keywords | TRANSFERASE / transketolase | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Scheffersomyces stipitis CBS 6054 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.101 Å | ||||||
Authors | Li, T.L. / Hsu, N.S. / Wang, Y.L. | ||||||
Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2018 Title: The Mesomeric Effect of Thiazolium on non-Kekule Diradicals in Pichia stipitis Transketolase. Authors: Hsu, N.S. / Wang, Y.L. / Lin, K.H. / Chang, C.F. / Lyu, S.Y. / Hsu, L.J. / Liu, Y.C. / Chang, C.Y. / Wu, C.J. / 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 | 5xtl.cif.gz | 291.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xtl.ent.gz | 229.7 KB | Display | PDB format |
PDBx/mmJSON format | 5xtl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xtl_validation.pdf.gz | 476.3 KB | Display | wwPDB validaton report |
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Full document | 5xtl_full_validation.pdf.gz | 478.5 KB | Display | |
Data in XML | 5xtl_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5xtl_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xtl ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xtl | HTTPS FTP |
-Related structure data
Related structure data | 5xryC 5xs6C 5xsaC 5xsbC 5xsmC 5xtvC 5xufC 5xvtC 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 75102.453 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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-Non-polymers , 5 types, 885 molecules
#2: Chemical | ChemComp-P23 / | ||||
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#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | #5: Chemical | ChemComp-8GF / | #6: 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: 3.11 Å3/Da / Density % sol: 60.43 % |
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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: Jan 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→30 Å / Num. obs: 369681 / % possible obs: 98.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.1→1.14 Å / Rmerge(I) obs: 0.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HYV Resolution: 1.101→27.622 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 15.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.101→27.622 Å
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Refine LS restraints |
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LS refinement shell |
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