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Yorodumi- PDB-4ff7: Structure of C126S mutant of Saccharomyces cerevisiae triosephosp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ff7 | ||||||
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Title | Structure of C126S mutant of Saccharomyces cerevisiae triosephosphate isomerase | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | OXIDOREDUCTASE / (ALFA/BETA )8 barrel / ISOMERASE | ||||||
Function / homology | Function and homology information Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Rodriguez-Romero, A. / Hernandez-Santoyo, A. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2012 Title: Effects of a buried cysteine-to-serine mutation on yeast triosephosphate isomerase structure and stability. Authors: Hernandez-Santoyo, A. / Dominguez-Ramirez, L. / Reyes-Lopez, C.A. / Gonzalez-Mondragon, E. / Hernandez-Arana, A. / Rodriguez-Romero, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ff7.cif.gz | 116.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ff7.ent.gz | 89 KB | Display | PDB format |
PDBx/mmJSON format | 4ff7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/4ff7 ftp://data.pdbj.org/pub/pdb/validation_reports/ff/4ff7 | HTTPS FTP |
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-Related structure data
Related structure data | 1ypiS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 26811.354 Da / Num. of mol.: 2 / Mutation: C126S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: TPI1, YDR050C, YD9609.05C / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: P00942, triose-phosphate isomerase |
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-Non-polymers , 6 types, 337 molecules
#2: Chemical | ChemComp-PGA / | ||||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NA / | #5: Chemical | #6: Chemical | #7: 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: 2.15 Å3/Da / Density % sol: 42.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Ammonium sulfate 2.2 M, 0.01 M cobaltous chloride hexahydrate in 0.01 M MES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9791 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2007 / Details: MIRRORS | |||||||||||||||||||||
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.86→40.49 Å / Num. all: 39667 / Num. obs: 39548 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 21.45 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.4 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YPI Resolution: 1.86→40.49 Å / SU ML: 0.21 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.3 / Phase error: 19.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.0189 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→40.49 Å
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Refine LS restraints |
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LS refinement shell |
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