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Yorodumi- PDB-1ngs: COMPLEX OF TRANSKETOLASE WITH THIAMIN DIPHOSPHATE, CA2+ AND ACCEP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ngs | ||||||
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Title | COMPLEX OF TRANSKETOLASE WITH THIAMIN DIPHOSPHATE, CA2+ AND ACCEPTOR SUBSTRATE ERYTHROSE-4-PHOSPHATE | ||||||
Components | TRANSKETOLASE | ||||||
Keywords | TRANSFERASE / THIAMINE PYROPHOSPHATE / MAGNESIUM / MULTIGENE FAMILY | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.4 Å | ||||||
Authors | Nilsson, U. / Lindqvist, Y. / Schneider, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1997 Title: Examination of substrate binding in thiamin diphosphate-dependent transketolase by protein crystallography and site-directed mutagenesis. Authors: Nilsson, U. / Meshalkina, L. / Lindqvist, Y. / Schneider, G. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Refined Structure of Transketolase from Saccharomyces Cerevisiae at 2.0 A Resolution Authors: Nikkola, M. / Lindqvist, Y. / Schneider, G. #2: Journal: Embo J. / Year: 1992 Title: Three-Dimensional Structure of Transketolase, a Thiamine Diphosphate Dependent Enzyme, at 2.5 A Resolution Authors: Lindqvist, Y. / Schneider, G. / Ermler, U. / Sundstrom, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ngs.cif.gz | 276.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ngs.ent.gz | 221 KB | Display | PDB format |
PDBx/mmJSON format | 1ngs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ngs_validation.pdf.gz | 516.4 KB | Display | wwPDB validaton report |
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Full document | 1ngs_full_validation.pdf.gz | 544 KB | Display | |
Data in XML | 1ngs_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 1ngs_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/1ngs ftp://data.pdbj.org/pub/pdb/validation_reports/ng/1ngs | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.788, -0.0005, -0.6156), Vector: |
-Components
#1: Protein | Mass: 73887.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Plasmid: PTKL1 / Gene (production host): TKL1 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23254, transketolase #2: Chemical | #3: Sugar | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.84 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.6 / Details: SEE THE PAPER, pH 7.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Schneider, G., (1989) J. Biol. Chem., 264, 21619. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. obs: 45990 / % possible obs: 81 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.062 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. measured all: 156468 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å |
-Processing
Software |
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Refinement | Resolution: 2.4→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: TWO-FOLD | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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