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Yorodumi- PDB-2jk2: STRUCTURAL BASIS OF HUMAN TRIOSEPHOSPHATE ISOMERASE DEFICIENCY. C... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jk2 | ||||||
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Title | STRUCTURAL BASIS OF HUMAN TRIOSEPHOSPHATE ISOMERASE DEFICIENCY. CRYSTAL STRUCTURE OF THE WILD TYPE ENZYME. | ||||||
Components | TRIOSEPHOSPHATE ISOMERASE | ||||||
Keywords | ISOMERASE / ALTERNATIVE SPLICING / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS / DISEASE MUTATION / PENTOSE SHUNT / PHOSPHOPROTEIN / GLUCONEOGENESIS / GLYCOLYSIS / ACETYLATION / POLYMORPHISM | ||||||
Function / homology | Function and homology information methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / canonical glycolysis / Glycolysis ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / glycolytic process / ubiquitin protein ligase binding / protein homodimerization activity / extracellular space / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
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. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 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, 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", "BA" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA", "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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jk2.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jk2.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 2jk2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jk/2jk2 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/2jk2 | HTTPS FTP |
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-Related structure data
Related structure data | 2vomC 1wyiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26714.400 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-249 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET3B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60174, triose-phosphate isomerase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 100 MM TRIS PH 8.5, 20% PEG MME2000, 10 MM NICL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 13, 2008 |
Radiation | Monochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. obs: 52549 / % possible obs: 97.2 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.048 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / Rsym value: 0.24 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1WYI Resolution: 1.7→92.85 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.448 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.95 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→92.85 Å
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