+Open data
-Basic information
Entry | Database: PDB / ID: 1nf0 | ||||||
---|---|---|---|---|---|---|---|
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 / COMO / Resolution: 1.6 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1nf0.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1nf0.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 1nf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/1nf0 ftp://data.pdbj.org/pub/pdb/validation_reports/nf/1nf0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1neyC 1i45S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 44.43 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.6→40 Å / Num. all: 62255 / Num. obs: 62255 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.6→1.66 Å / % possible all: 95.5 |
Reflection | *PLUS Highest resolution: 1.6 Å / Num. measured all: 231083 / Rmerge(I) obs: 0.065 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: COMO Starting model: pdb entry 1I45 Resolution: 1.6→40 Å / Num. parameters: 17233 / Num. restraintsaints: 16005 / 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
| |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 4194.32 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |