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- PDB-2ypi: CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ypi | ||||||
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Title | CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-ANGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | TRIOSE PHOSPHATE ISOMERASE | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Lolis, E. / Petsko, G.A. | ||||||
![]() | ![]() Title: Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis. Authors: Lolis, E. / Petsko, G.A. #1: ![]() 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. #2: ![]() Title: Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a (Double Quote)Simple(Double Quote) Enzyme (Question Mark) Authors: Alber, T.C. / Davenportjunior, R.C. / Giammona, D.A. / Lolis, E. / Petsko, G.A. / Ringe, D. #3: ![]() 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. #4: ![]() 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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Remark 700 | SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.8 KB | Display | ![]() |
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PDB format | ![]() | 67.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.5 KB | Display | ![]() |
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Full document | ![]() | 498.4 KB | Display | |
Data in XML | ![]() | 25.8 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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: (-0.9976, -0.06946, -6.0E-5), Vector: Details | THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. | |
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Components
#1: Protein | Mass: 26696.225 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P00942, triose-phosphate isomerase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE RESIDUE NUMBERING IN EACH CHAIN IS SEQUENTIAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.79 % | ||||||||||||||||||||
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Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Rmerge(I) obs: 0.084 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.177 / Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 10355 / Highest resolution: 2.5 Å / Rfactor obs: 0.177 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.8 Å / Num. reflection obs: 2037 / Rfactor obs: 0.164 |