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- PDB-5brb: Crystal structure of Q64E mutant of Triosephosphate isomerase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5brb | ||||||
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Title | Crystal structure of Q64E mutant of Triosephosphate isomerase from Plasmodium falciparum | ||||||
![]() | 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 | ![]() ![]() | ||||||
![]() | Bandyopadhyay, D. / Murthy, M.R.N. / Balaram, H. / Balaram, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Probing the role of highly conserved residues in triosephosphate isomerase - analysis of site specific mutants at positions 64 and 75 in the Plasmodial enzyme Authors: Bandyopadhyay, D. / 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 | ![]() | 105.4 KB | Display | ![]() |
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PDB format | ![]() | 78.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 430.5 KB | Display | ![]() |
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Full document | ![]() | 430.5 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zz9C ![]() 5bmwC ![]() 5bmxC ![]() 5bnkC ![]() 1o5xS 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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Unit cell |
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Components
#1: Protein | Mass: 27998.723 Da / Num. of mol.: 2 / Mutation: Q64E, A163V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TPI / Plasmid: pTrc99A / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.68 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 28% PEG 1450, 100mM HEPES, 10mM calcium chloride, 0.5mM DTT, 0.5mM sodium azide |
-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: Sep 7, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.526→75.35 Å / Num. all: 14204 / Num. obs: 14204 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 40 Å2 / Rpim(I) all: 0.101 / Rrim(I) all: 0.187 / Rsym value: 0.156 / Net I/av σ(I): 4.151 / Net I/σ(I): 5.6 / Num. measured all: 45770 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1O5X Resolution: 2.53→73.57 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.819 / WRfactor Rfree: 0.2917 / WRfactor Rwork: 0.2309 / FOM work R set: 0.7651 / SU B: 16.25 / SU ML: 0.35 / SU Rfree: 0.3982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 39.95 Å2 / Biso mean: 23.718 Å2 / Biso min: 8.73 Å2
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Refinement step | Cycle: final / Resolution: 2.53→73.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.526→2.591 Å / Total num. of bins used: 20
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