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- PDB-4z0s: F96A Mutant of Plasmodium Falciparum Triosephosphate Isomerase -

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Basic information

Entry
Database: PDB / ID: 4z0s
TitleF96A 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: 2.39 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,2789
Polymers55,8432
Non-polymers4347
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-23 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.420, 76.840, 76.570
Angle α, β, γ (deg.)90.00, 99.44, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 2 - 248 / Label seq-ID: 2 - 248

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 27921.641 Da / Num. of mol.: 2 / Mutation: F96A,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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: NaOAc, 10mM Li2SO4, 0.5mM DTT, 0.5mM NaN3, 0.5mM EDTA, 24% PEG 1450

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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: Jan 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.36→53.87 Å / Num. obs: 17068 / % possible obs: 92 % / Redundancy: 3.6 % / Net I/σ(I): 17
Reflection shellResolution: 2.36→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.4 / % possible all: 70

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M7P

1m7p


Resolution: 2.39→53.87 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.871 / SU B: 10.799 / SU ML: 0.25 / Cross valid method: THROUGHOUT / ESU R: 1.03 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27122 861 5.1 %RANDOM
Rwork0.2276 ---
obs0.22992 16173 94.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.165 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.04 Å2
2--0 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.39→53.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3653 0 28 81 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193735
X-RAY DIFFRACTIONr_bond_other_d0.0030.023416
X-RAY DIFFRACTIONr_angle_refined_deg1.121.9355037
X-RAY DIFFRACTIONr_angle_other_deg0.89737790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01424.94166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11115590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0171516
X-RAY DIFFRACTIONr_chiral_restr0.0630.2567
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024354
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02878
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_it1.0523.0091950
X-RAY DIFFRACTIONr_mcbond_other1.0533.0091949
X-RAY DIFFRACTIONr_mcangle_it1.8094.5082431
X-RAY DIFFRACTIONr_mcangle_other1.8094.5082432
X-RAY DIFFRACTIONr_scbond_it0.7532.9561785
X-RAY DIFFRACTIONr_scbond_other0.7522.9561785
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3184.422607
X-RAY DIFFRACTIONr_long_range_B_refined3.09923.6754184
X-RAY DIFFRACTIONr_long_range_B_other3.09223.6894181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12000 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 60 -
Rwork0.252 1133 -
obs--89.77 %

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