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Yorodumi- PDB-3ypi: ELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ypi | ||||||
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Title | ELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF HISTIDINE-95 | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) | ||||||
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 / Resolution: 2.8 Å | ||||||
Authors | Lolis, E. / Petsko, G.A. | ||||||
Citation | Journal: Biochemistry / Year: 1991 Title: Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95. Authors: Komives, E.A. / Chang, L.C. / Lolis, E. / Tilton, R.F. / Petsko, G.A. / Knowles, J.R. #1: Journal: Biochemistry / Year: 1990 Title: Crystallographic Analysis of the Complex between Triosephosphate Isomerase and 2-Phosphoglycolate at 2.5-Angstroms Resolution. Implications for Catalysis Authors: Lolis, E. / Petsko, G.A. #2: Journal: Biochemistry / Year: 1990 Title: Structure of Yeast Triosephosphate Isomerase at 1.9-Angstroms Resolution Authors: Lolis, E. / Alber, T. / Davenport, R.C. / Rose, D. / Hartman, F.C. / Petsko, G.A. #3: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1987 Title: Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a "Simple" Enzyme? Authors: Alber, T.C. / Davenportjunior, R.C. / Giammona, D.A. / Lolis, E. / Petsko, G.A. / Ringe, D. #4: Journal: J.Biol.Chem. / Year: 1981 Title: Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation Authors: Alber, T. / Hartman, F.C. / Johnson, R.M. / Petsko, G.A. / Tsernoglou, D. #5: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981 Title: On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase Authors: Alber, T. / Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D. / Rivers, P.S. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ypi.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ypi.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ypi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/3ypi ftp://data.pdbj.org/pub/pdb/validation_reports/yp/3ypi | HTTPS FTP |
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-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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-Components
#1: Protein | Mass: 26686.205 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cell line: 293 / Strain (production host): 293 / References: UniProt: P00942, triose-phosphate isomerase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.81 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.8 / Method: other | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.8 Å |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.184 / Highest resolution: 2.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.8 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 9635 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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