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Open data
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Basic information
Entry | Database: PDB / ID: 1nf0 | ||||||
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Title | Triosephosphate Isomerase in Complex with DHAP | ||||||
![]() | triosephosphate isomerase | ||||||
![]() | ISOMERASE / yeast / triosephosphate isomerase / DHAP / dihydroxyacetone phosphate / michaelis complex | ||||||
Function / homology | ![]() Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jogl, G. / Rozovsky, S. / McDermott, A.E. / Tong, L. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.6 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441 KB | Display | ![]() |
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Full document | ![]() | 450.8 KB | Display | |
Data in XML | ![]() | 26 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1neyC ![]() 1i45S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: TPI1 / Plasmid: PKK223-3 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 44.43 % | ||||||||||||||||||||||||||||||||||||||||||
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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: ![]() ![]() ![]() |
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 |
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Processing
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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
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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
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Refine LS restraints |
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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 |