+Open data
-Basic information
Entry | Database: PDB / ID: 1ney | ||||||
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Title | Triosephosphate Isomerase in Complex with DHAP | ||||||
Components | triosephosphate isomerase | ||||||
Keywords | ISOMERASE / yeast / triosephosphate isomerase / DHAP / dihydroxyacetone phosphate / michaelis complex | ||||||
Function / homology | Function and homology information Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Jogl, G. / Rozovsky, S. / McDermott, A.E. / Tong, L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2-A resolution. Authors: Jogl, G. / Rozovsky, S. / McDermott, A.E. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ney.cif.gz | 310 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ney.ent.gz | 255.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ney.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/1ney ftp://data.pdbj.org/pub/pdb/validation_reports/ne/1ney | HTTPS FTP |
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-Related structure data
Related structure data | 1nf0C 1i45S 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: 26652.146 Da / Num. of mol.: 2 / Mutation: W90Y, W157F, W168(FTR) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TPI1 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JA300 / References: UniProt: P00942, triose-phosphate isomerase #2: Chemical | #3: 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: 1.79 Å3/Da / Density % sol: 31.2 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: evaporation, recrystallization / pH: 6.8 Details: 50mM TRIS, 50mM NaCl, 20%PEG 4000, 30mM DHAP, pH 6.8, EVAPORATION, RECRYSTALLIZATION, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method / Details: Rozovsky, S., (2001) J. Mol. Biol., 310, 271. | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.928 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 4, 2001 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→30 Å / Num. all: 134020 / Num. obs: 134020 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.237 / % possible all: 91.3 |
Reflection | *PLUS Highest resolution: 1.2 Å / Num. measured all: 285716 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1I45 Resolution: 1.2→30 Å / Num. parameters: 41314 / Num. restraintsaints: 71814 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28(1995) 53-56
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Refine analyze | Num. disordered residues: 16 / Occupancy sum hydrogen: 3790.7 / Occupancy sum non hydrogen: 4548.7 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.2 Å / Lowest resolution: 30 Å / Rfactor Rfree: 0.15 / Rfactor Rwork: 0.125 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |