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- PDB-5brb: Crystal structure of Q64E mutant of Triosephosphate isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 5brb
TitleCrystal structure of Q64E mutant of Triosephosphate isomerase from Plasmodium falciparum
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / identical protein binding / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsBandyopadhyay, D. / Murthy, M.R.N. / Balaram, H. / Balaram, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Febs J. / Year: 2015
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
DepositionMay 30, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0434
Polymers55,9972
Non-polymers462
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-40 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.020, 75.350, 74.130
Angle α, β, γ (deg.)90.000, 97.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 27998.723 Da / Num. of mol.: 2 / Mutation: Q64E, A163V
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 ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.68 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 1450, 100mM HEPES, 10mM calcium chloride, 0.5mM DTT, 0.5mM sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 7, 2013
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 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: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.51-2.6530.4412.3521517340.2980.4412.381.4
2.65-2.813.20.3552.1638419900.2340.355399.9
2.81-33.20.2732.7614319010.1790.2733.9100
3-3.253.30.2113.4570617530.1380.2114.8100
3.25-3.563.30.1574.4529816220.1010.1576.3100
3.56-3.973.30.1265.3479214620.0810.1267.7100
3.97-4.593.30.1085.9425812920.0690.1088.6100
4.59-5.623.30.1075.8366011170.0680.1078.6100
5.62-7.953.30.0966.727938540.0610.096899.9
7.95-73.4583.20.0925.715214790.0610.0929.499.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5X

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2927 714 5 %RANDOM
Rwork0.2288 ---
obs0.232 13474 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 39.95 Å2 / Biso mean: 23.718 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å2-0 Å2-0.63 Å2
2---0.34 Å2-0 Å2
3---1.38 Å2
Refinement stepCycle: final / Resolution: 2.53→73.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3667 0 2 69 3738
Biso mean--37.04 18.1 -
Num. residues----486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193727
X-RAY DIFFRACTIONr_bond_other_d0.0010.023459
X-RAY DIFFRACTIONr_angle_refined_deg1.071.9435051
X-RAY DIFFRACTIONr_angle_other_deg0.8737905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05825.207169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49115607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2321516
X-RAY DIFFRACTIONr_chiral_restr0.0570.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024327
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02859
X-RAY DIFFRACTIONr_mcbond_it0.4072.4861940
X-RAY DIFFRACTIONr_mcbond_other0.4062.4861939
X-RAY DIFFRACTIONr_mcangle_it0.7143.7262415
LS refinement shellResolution: 2.526→2.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 47 -
Rwork0.349 829 -
all-876 -
obs--80.96 %

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