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- PDB-4z0j: F96S/S73A Double mutant of Plasmodium Falciparum Triosephosphate ... -

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Basic information

Entry
Database: PDB / ID: 4z0j
TitleF96S/S73A Double mutant of Plasmodium Falciparum Triosephosphate Isomerase
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM BARRELS / BETA-ALPHA BARRELS / GLYCOLYSIS
Function / homology
Function and homology information


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
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: 2.07 Å
AuthorsPareek, V. / Balaram, P. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DEPARTMENT OF SCIENCE AND TECHNOLOGY India
CitationJournal: Chembiochem / Year: 2016
Title: Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme
Authors: Pareek, V. / Samanta, M. / Joshi, N.V. / Balaram, H. / Murthy, M.R.N. / Balaram, P.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Nov 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)56,87617
Polymers55,8432
Non-polymers1,03315
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-65 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.480, 50.840, 88.260
Angle α, β, γ (deg.)90.00, 91.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 27921.641 Da / Num. of mol.: 2 / Mutation: F96S,S73A,A163V
Source method: isolated from a genetically manipulated source
Details: Mutation of A163V present in the wild type TIM considered as template
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: TPI / Plasmid: pTrc99A / Details (production host): PARC1008 / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: NaOAc, 10mM Li2SO4, 0.5mM DTT, 0.5mM NaN3, 0.5mM EDTA, 28% PEG 1450

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.07→53.45 Å / Num. obs: 29180 / % possible obs: 98.9 % / Redundancy: 3.3 % / Net I/σ(I): 7
Reflection shellResolution: 2.07→2.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.8 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VFD

2vfd


Resolution: 2.07→53.45 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.843 / SU B: 5.291 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.28 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26011 1471 5 %RANDOM
Rwork0.2165 ---
obs0.21873 27919 93.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.437 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.07→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3840 0 63 301 4204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193960
X-RAY DIFFRACTIONr_bond_other_d0.0010.023782
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.9535336
X-RAY DIFFRACTIONr_angle_other_deg0.73738690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.975495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41325.514185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28815706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9641516
X-RAY DIFFRACTIONr_chiral_restr0.0620.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02894
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2810.931967
X-RAY DIFFRACTIONr_mcbond_other0.2810.931966
X-RAY DIFFRACTIONr_mcangle_it0.5071.3942456
X-RAY DIFFRACTIONr_mcangle_other0.5071.3942457
X-RAY DIFFRACTIONr_scbond_it0.2340.9611993
X-RAY DIFFRACTIONr_scbond_other0.2350.9641981
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.41.4232852
X-RAY DIFFRACTIONr_long_range_B_refined2.0557.5824775
X-RAY DIFFRACTIONr_long_range_B_other2.0557.5844776
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 30 -
Rwork0.261 478 -
obs--21.98 %

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