+Open data
-Basic information
Entry | Database: PDB / ID: 6c2g | ||||||
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Title | Human triosephosphate isomerase mutant V231M | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE | ||||||
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: 2.3 Å | ||||||
Authors | Torres, L.A. / Enriquez, F.S. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Differential effects on enzyme stability and kinetic parameters of mutants related to human triosephosphate isomerase deficiency. Authors: Cabrera, N. / Torres-Larios, A. / Garcia-Torres, I. / Enriquez-Flores, S. / Perez-Montfort, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6c2g.cif.gz | 375.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6c2g.ent.gz | 311 KB | Display | PDB format |
PDBx/mmJSON format | 6c2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/6c2g ftp://data.pdbj.org/pub/pdb/validation_reports/c2/6c2g | HTTPS FTP |
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-Related structure data
Related structure data | 2jk2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0 / Auth seq-ID: 4 - 247 / Label seq-ID: 5 - 248
NCS ensembles :
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-Components
#1: Protein | Mass: 26733.531 Da / Num. of mol.: 4 / Mutation: V231M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPI1, TPI / Variant: V231M / Plasmid: pET3a Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) 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: 2.55 Å3/Da / Density % sol: 51.83 % / Description: 100X100X200 micrometers |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.987 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→41.89 Å / Num. obs: 46899 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 32.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 4502 / CC1/2: 0.79 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JK2 Resolution: 2.3→41.89 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.928 / SU B: 15.175 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.368 / ESU R Free: 0.219 / 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: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.244 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→41.89 Å
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Refine LS restraints |
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