+Open data
-Basic information
Entry | Database: PDB / ID: 1gpu | ||||||
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Title | Transketolase complex with reaction intermediate | ||||||
Components | TRANSKETOLASE 1 | ||||||
Keywords | TRANSFERASE / TRANSFERASE(KETONE RESIDUES) | ||||||
Function / homology | Function and homology information transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Fiedler, E. / Thorell, S. / Sandalova, T. / Koenig, S. / Schneider, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2002 Title: Snapshot of a Key Intermediate in Enzymatic Thiamin Catalysis: Crystal Structure of the Alpha-Carbanion of (Alpha,Beta-Dihydroxyethyl)-Thiamin Diphosphate in the Active Site of Transketolase ...Title: Snapshot of a Key Intermediate in Enzymatic Thiamin Catalysis: Crystal Structure of the Alpha-Carbanion of (Alpha,Beta-Dihydroxyethyl)-Thiamin Diphosphate in the Active Site of Transketolase from Saccharomyces Cerevisiae. Authors: Fiedler, E. / Thorell, S. / Sandalova, T. / Golbik, R. / Koenig, S. / Schneider, G. #1: Journal: Biochemistry / Year: 1997 Title: Identification of Catalytically Important Residues in Yeast Transketolase. Authors: Wikner, C. / Nilsson, U. / Meshalkina, L. / Udekwu, C. / Lindqvist, Y. / Schneider, G. #2: Journal: Eur.J.Biochem. / Year: 1997 Title: Examination of the Thiamin Diphosphate Binding Site in Yeasttransketolase by Site-Directed Mutagenesis Authors: Meshalkina, L. / Nilsson, U. / Wikner, C. / Kostikowa, T. #3: Journal: Science / Year: 1997 Title: How Thiamin Diphosphateis Activated in Enzyme Authors: Kern, D. / Kern, G. / Neef, H. / Tittmann, K. / Killenberg-Jabs, M. / Wikner, C. / Schneider, G. #4: Journal: J.Mol.Biol. / Year: 1994 Title: Refined Structure of Transketolase from Saccharomyces Cerevisiae at 2.0 Angstroms Resolution Authors: Nikkola, M. / Lindqvist, Y. / Schneider, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gpu.cif.gz | 284.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gpu.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 1gpu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/1gpu ftp://data.pdbj.org/pub/pdb/validation_reports/gp/1gpu | HTTPS FTP |
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-Related structure data
Related structure data | 1trkS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.787981, 0.002369, -0.615696), Vector: |
-Components
#1: Protein | Mass: 73887.391 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P23254, transketolase #2: Chemical | #3: Chemical | #4: 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: 2.27 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.9 / Details: pH 7.90 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8459 |
Detector | Date: Apr 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8459 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→30 Å / Num. obs: 104364 / % possible obs: 92.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.86→1.89 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 3.5 / % possible all: 89 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 333802 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TRK Resolution: 1.86→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: DENSITY MODIFICATION / Bsol: 59.9 Å2 / ksol: 0.404 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.87 Å / Total num. of bins used: 50 /
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |