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- PDB-4yxg: F96Y Mutant of Plasmodium Falciparum Triosephosphate Isomerase -

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Basic information

Entry
Database: PDB / ID: 4yxg
TitleF96Y 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 / 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: 1.9 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 23, 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)56,52410
Polymers56,0272
Non-polymers4978
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-4 kcal/mol
Surface area18590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.000, 70.320, 72.580
Angle α, β, γ (deg.)90.00, 101.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28013.738 Da / Num. of mol.: 2 / Mutation: F96Y,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.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 3.6 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 1450, HEPES, 10mM CaCl2, 0.5mM DTT, 0.5mM NaN3, 0.5mM EDTA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.9→36.2 Å / Num. obs: 28683 / % possible obs: 99 % / Redundancy: 3 % / Net I/σ(I): 15
Reflection shellResolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.3 / % possible all: 99

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Processing

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

2vfh


Resolution: 1.9→35.51 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 3.736 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22432 1454 5.1 %RANDOM
Rwork0.18033 ---
obs0.18257 27191 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 32 170 3816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193709
X-RAY DIFFRACTIONr_bond_other_d0.0010.023446
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.9474995
X-RAY DIFFRACTIONr_angle_other_deg0.73637904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6185475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41125.181166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04615624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4131514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02842
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_it0.5921.7551900
X-RAY DIFFRACTIONr_mcbond_other0.5921.7541899
X-RAY DIFFRACTIONr_mcangle_it1.0242.6212365
X-RAY DIFFRACTIONr_mcangle_other1.0232.6212366
X-RAY DIFFRACTIONr_scbond_it0.5671.7881809
X-RAY DIFFRACTIONr_scbond_other0.5671.7881809
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9452.6492622
X-RAY DIFFRACTIONr_long_range_B_refined2.24414.0594318
X-RAY DIFFRACTIONr_long_range_B_other2.24414.0634319
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 120 -
Rwork0.214 1988 -
obs--98.78 %

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