+Open data
-Basic information
Entry | Database: PDB / ID: 4zvj | ||||||
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Title | Structure of human triose phosphate isomerase K13M | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / Triose phosphate isomerase / TIM / dimer / glycolysis | ||||||
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: 1.6996 Å | ||||||
Authors | Amrich, C.G. / Smith, C. / Heroux, A. / VanDemark, A.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2015 Title: Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency. Authors: Roland, B.P. / Amrich, C.G. / Kammerer, C.J. / Stuchul, K.A. / Larsen, S.B. / Rode, S. / Aslam, A.A. / Heroux, A. / Wetzel, R. / VanDemark, A.P. / Palladino, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zvj.cif.gz | 294.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zvj.ent.gz | 242.2 KB | Display | PDB format |
PDBx/mmJSON format | 4zvj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zv/4zvj ftp://data.pdbj.org/pub/pdb/validation_reports/zv/4zvj | HTTPS FTP |
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-Related structure data
Related structure data | 4pocSC 4podC S: Starting model for refinement C: citing same article (ref.) |
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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: 27228.029 Da / Num. of mol.: 2 / Mutation: K13M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon+ RILP / References: UniProt: P60174, triose-phosphate isomerase #2: Chemical | ChemComp-NA / | #3: Chemical | ChemComp-K / | #4: 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: 2.09 Å3/Da / Density % sol: 41.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 35% PEG 2000 MME, 50 mM KBr, Tris pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 5, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6996→50 Å / Num. obs: 49677 / % possible obs: 100 % / Redundancy: 12.3 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.063 / Χ2: 0.896 / Net I/av σ(I): 42.049 / Net I/σ(I): 8.5 / Num. measured all: 608944 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4POC Resolution: 1.6996→11.995 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.09 Å2 / Biso mean: 31.7994 Å2 / Biso min: 12.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6996→11.995 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18
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