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- PDB-2vom: Structural basis of human triosephosphate isomerase deficiency. M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2vom | ||||||
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Title | Structural basis of human triosephosphate isomerase deficiency. Mutation E104D and correlation to solvent perturbation. | ||||||
![]() | TRIOSEPHOSPHATE ISOMERASE | ||||||
![]() | ISOMERASE / ALTERNATIVE SPLICING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / DISEASE MUTATION / PENTOSE SHUNT / PHOSPHOPROTEIN / GLUCONEOGENESIS / GLYCOLYSIS / ACETYLATION / POLYMORPHISM | ||||||
Function / homology | ![]() methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / glycerol catabolic process / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / canonical glycolysis / glycerol catabolic process / Glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rodriguez-Almazan, C. / Arreola-Alemon, R. / Rodriguez-Larrea, D. / Aguirre-Lopez, B. / de Gomez-Puyou, M.T. / Perez-Montfort, R. / Costas, M. / Gomez-Puyou, A. / Torres-Larios, A. | ||||||
![]() | ![]() Title: Structural Basis of Human Triosephosphate Isomerase Deficiency: Mutation E104D is Related to Alterations of a Conserved Water Network at the Dimer Interface. Authors: Rodriguez-Almazan, C. / Arreola-Alemon, R. / Rodriguez-Larrea, D. / Aguirre-Lopez, B. / De Gomez-Puyou, M.T. / Perez-Montfort, R. / Costas, M. / Gomez-Puyou, A. / Torres-Larios, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-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 | ![]() | 201.5 KB | Display | ![]() |
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PDB format | ![]() | 162.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.9 KB | Display | ![]() |
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Full document | ![]() | 477.1 KB | Display | |
Data in XML | ![]() | 43.4 KB | Display | |
Data in CIF | ![]() | 61.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2jk2C ![]() 1wyiS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 26700.373 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-249 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 105 TO ASP ENGINEERED RESIDUE IN CHAIN B, GLU 105 TO ASP ...ENGINEERED | Sequence details | THE STRUCTURE CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 100 MM TRIS PH 8.5, 20% PEG MME2000, 4% POLYPROPYLENE GLYCOL P400, 10 MM NICL2 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 20, 2007 Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR |
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→60.2 Å / Num. obs: 81960 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.11 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.57 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.32 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WYI Resolution: 1.85→50 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: CHAIN D IS MORE DISORDERED THAN CHAINS A, B AND C ON RESIDUES 1 THIS IS PROBABLY DUE TO LACK OF CRYSTALLOGRAPHIC CONTACTS
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Solvent computation | Solvent model: CNS BULK SOLVENT MODEL / Bsol: 36.303 Å2 / ksol: 0.351707 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.92 Å / Total num. of bins used: 10
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Xplor file |
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