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Yorodumi- PDB-3py2: Structure of C126S mutant of Plasmodium falciparum triosephosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3py2 | ||||||
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Title | Structure of C126S mutant of Plasmodium falciparum triosephosphate isomerase | ||||||
Components | Triosephosphate isomerase | ||||||
Keywords | ISOMERASE / TIM barrel | ||||||
Function / homology | Function and homology information triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / identical protein binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | ||||||
Authors | Samanta, M. / Banerjee, M. / Murthy, M.R.N. / Balaram, H. / Balaram, P. | ||||||
Citation | Journal: Febs J. / Year: 2011 Title: Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis--distal effects on dimer stability. Authors: Samanta, M. / Banerjee, M. / Murthy, M.R. / Balaram, H. / Balaram, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3py2.cif.gz | 119.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3py2.ent.gz | 93.1 KB | Display | PDB format |
PDBx/mmJSON format | 3py2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/py/3py2 ftp://data.pdbj.org/pub/pdb/validation_reports/py/3py2 | 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: 27981.674 Da / Num. of mol.: 2 / Mutation: C126S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: TPI / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase #2: Chemical | #3: Chemical | ChemComp-EDO / | #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: 2.11 Å3/Da / Density % sol: 41.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 24% PEG, 1M HEPES bufffer (pH 7.0), 10mM Lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 31, 2009 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→48.77 Å / Num. all: 31302 / Num. obs: 31243 / % possible obs: 85.01 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.67 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.39 |
Reflection shell | Resolution: 1.93→1.98 Å / % possible all: 77.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→43.45 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.902 / SU B: 3.424 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.179 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.166 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→43.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.933→1.983 Å / Total num. of bins used: 20
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