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- PDB-5bmx: Crystal structure of T75N mutant of Triosephosphate isomerase fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5bmx | ||||||
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Title | Crystal structure of T75N 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 | ![]() | 223 KB | Display | ![]() |
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PDB format | ![]() | 175.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zz9C ![]() 5bmwC ![]() 5bnkC ![]() 5brbC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28010.736 Da / Num. of mol.: 4 / Mutation: T75N, A163V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: TPI / Plasmid: pTrc99A / Production host: ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 28% PEG 1450, 100mM Tris-HCl, 10mM Lithium sulphate, 0.5mM EDTA, 0.5mM DTT, 0.5mM sodium azide |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→91.748 Å / Num. all: 88535 / Num. obs: 88535 / % possible obs: 97.2 % / Redundancy: 7.5 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.124 / Rsym value: 0.116 / Net I/av σ(I): 4.014 / Net I/σ(I): 11.3 / Num. measured all: 668294 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1O5X Resolution: 1.8→91.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2231 / WRfactor Rwork: 0.1726 / FOM work R set: 0.8567 / SU B: 2.518 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1292 / SU Rfree: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 58.95 Å2 / Biso mean: 15.687 Å2 / Biso min: 4.95 Å2
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Refinement step | Cycle: final / Resolution: 1.8→91.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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