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- PDB-3pvf: Structure of C126S mutant of Plasmodium falciparum triosephosphat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pvf | ||||||
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Title | Structure of C126S mutant of Plasmodium falciparum triosephosphate isomerase complexed with PGA | ||||||
![]() | Triosephosphate isomerase | ||||||
![]() | ISOMERASE / Tim barrel | ||||||
Function / homology | ![]() triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Samanta, M. / Banerjee, M. / Murthy, M.R.N. / Balaram, H. / Balaram, P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71 KB | Display | ![]() |
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PDB format | ![]() | 51.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424 KB | Display | ![]() |
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Full document | ![]() | 425 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pwaC ![]() 3py2C ![]() 1lyxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27981.674 Da / Num. of mol.: 1 / Mutation: C126S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TPI / Plasmid: pTrc99A / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-PGA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG, HEPES buffer(pH 7.5), 10mM Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 30, 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: 1.73→38.91 Å / Num. obs: 25341 / % possible obs: 93.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.13 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 17.37 |
Reflection shell | Resolution: 1.732→1.777 Å / Rmerge(I) obs: 0.125 / % possible all: 83.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1LYX Resolution: 1.73→26.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.991 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / 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: 10.673 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→26.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.732→1.777 Å / Total num. of bins used: 20
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