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Yorodumi- PDB-6up5: Triosephosphate isomerase deficiency: Effect of F240L mutation on... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6up5 | ||||||
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Title | Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / glycolytic enzyme / alpha beta barrel | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.92 Å | ||||||
Authors | Romero, J.M. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2020 Title: Triosephosphate isomerase deficiency: Effect of F240L mutation on enzyme structure. Authors: Romero, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6up5.cif.gz | 114.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6up5.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 6up5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/6up5 ftp://data.pdbj.org/pub/pdb/validation_reports/up/6up5 | HTTPS FTP |
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-Related 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: 26983.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Production host: Escherichia coli (E. coli) References: UniProt: P60174, triose-phosphate isomerase, methylglyoxal synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.14 Å3/Da / Density % sol: 42.52 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 20% PEG 4000, and 10% 2-propanol PH range: 7.0-8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.4586 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.92→58.15 Å / Num. obs: 34287 / % possible obs: 97.6 % / Redundancy: 2.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.038 / Rrim(I) all: 0.068 / Net I/σ(I): 12.7 / Num. measured all: 97605 / Scaling rejects: 17 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.92→58.15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.123 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.164 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.58 Å2 / Biso mean: 24.855 Å2 / Biso min: 10.04 Å2
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Refinement step | Cycle: final / Resolution: 1.92→58.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.922→1.972 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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