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- PDB-5gv4: Y74COX MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 5gv4
TitleY74COX MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM BARREL / BETA-ALPHA BARRELS / GLYCOLYSIS / COVALENT DIMER
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / identical protein binding
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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsPareek, V. / Balaram, P. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science and Technology, Ministry of Science and Technology, India India
CitationJournal: To Be Published
Title: Y74COX MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE
Authors: Pareek, V. / Balaram, P. / Murthy, M.R.N.
History
DepositionSep 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4047
Polymers27,9381
Non-polymers4666
Water2,900161
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,80814
Polymers55,8752
Non-polymers93312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4200 Å2
ΔGint-24 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.620, 65.620, 141.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-421-

HOH

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Components

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


Mass: 27937.707 Da / Num. of mol.: 1 / Mutation: Y74C, 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 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: MES 100 mM, PEG 8K 18%, EDTA (10 mM), CaCl2 (10 mM), Sodium Azide 0.006%, 10% Ethylene glycol, Phosphoglycolic acid (50x molar excess)
PH range: 6.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.07→48.14 Å / Num. obs: 19232 / % possible obs: 97.2 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.2
Reflection shellResolution: 2.07→2.12 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.41 / % possible all: 64.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VFH

2vfh


Resolution: 2.09→19.85 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 4.369 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.17
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 980 5.2 %RANDOM
Rwork0.19784 ---
obs0.19979 18040 98.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.992 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.09→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1868 0 29 162 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191930
X-RAY DIFFRACTIONr_bond_other_d0.0020.021823
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9512599
X-RAY DIFFRACTIONr_angle_other_deg0.76434175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3155247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05825.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57215330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.985158
X-RAY DIFFRACTIONr_chiral_restr0.0740.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.085→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 75 -
Rwork0.25 1222 -
obs--93.85 %

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