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Yorodumi- PDB-3pf3: Crystal structure of a mutant (C202A) of Triosephosphate isomeras... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pf3 | ||||||
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Title | Crystal structure of a mutant (C202A) of Triosephosphate isomerase from Giardia lamblia derivatized with MMTS | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TRIOSEPHOSPHATE ISOMERASE / GIARDIA / ALPHA/BETA BARREL / THIOMETHYLATION / ALFA/BETA BARREL / THIOMETHYLATION OF CYS14 / CYS222 / CYS 228 | ||||||
Function / homology | Function and homology information methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm Similarity search - Function | ||||||
Biological species | Giardia intestinalis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.098 Å | ||||||
Authors | Enriquez-Flores, S. / Rodriguez-Romero, A. / Hernandez-Santoyo, A. / Reyes-Vivas, H. | ||||||
Citation | Journal: Proteins / Year: 2011 Title: Determining the molecular mechanism of inactivation by chemical modification of triosephosphate isomerase from the human parasite Giardia lamblia: A study for antiparasitic drug design. Authors: Enriquez-Flores, S. / Rodriguez-Romero, A. / Hernandez-Alcantara, G. / Oria-Hernandez, J. / Gutierrez-Castrellon, P. / Perez-Hernandez, G. / Mora-Ide, L. / Castillo-Villanueva, A. / Garcia- ...Authors: Enriquez-Flores, S. / Rodriguez-Romero, A. / Hernandez-Alcantara, G. / Oria-Hernandez, J. / Gutierrez-Castrellon, P. / Perez-Hernandez, G. / Mora-Ide, L. / Castillo-Villanueva, A. / Garcia-Torres, I. / Mendez, S.T. / Gomez-Manzo, S. / Torres-Arroyo, A. / Lopez-Velazquez, G. / Reyes-Vivas, H. #1: Journal: J.Mol.Biol. / Year: 2007 Title: Disulfide bridges in the mesophilic triosephosphate isomerase from Giardia lamblia are related to oligomerization and activity. Authors: Reyes-Vivas, H. / Diaz, A. / Peon, J. / Mendoza-Hernandez, G. / Hernandez-Alcantara, G. / De la Mora-De la Mora, I. / Enriquez-Flores, S. / Dominguez-Ramirez, L. / Lopez-Velazquez, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pf3.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pf3.ent.gz | 50.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/3pf3 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/3pf3 | HTTPS FTP |
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-Related structure data
Related structure data | 2dp3S 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28046.400 Da / Num. of mol.: 1 / Mutation: C202A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: WB STRAIN / Gene: GLTIM / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: P36186, triose-phosphate isomerase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 5MICROL OF C202A (13MG/ML) DISSOLVED IN 100MM TRIETHANOLAMINE, 10MM EDTA, MIXED WITH 5MICROL OF 2M AMMONIUM SULFATE,5% ISOPROPANOL, pH 7.4. Crystals were soaked with S-methyl ...Details: 5MICROL OF C202A (13MG/ML) DISSOLVED IN 100MM TRIETHANOLAMINE, 10MM EDTA, MIXED WITH 5MICROL OF 2M AMMONIUM SULFATE,5% ISOPROPANOL, pH 7.4. Crystals were soaked with S-methyl methanethiosulfonate (MMTS), VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 27, 2008 |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.098→38.9 Å / Num. all: 20618 / Num. obs: 20391 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 8.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2DP3 Resolution: 2.098→38.901 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.098→38.901 Å
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Refine LS restraints |
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LS refinement shell |
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