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

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Basic information

Entry
Database: PDB / ID: 5gzp
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 / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPareek, V. / Balaram, P. / Murthy, M.R.N.
CitationJournal: To Be Published
Title: Y74COX MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE ISOMERASE
Authors: Pareek, V. / Balaram, P. / Murthy, M.R.N.
History
DepositionSep 30, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)56,87015
Polymers55,8752
Non-polymers99513
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-20 kcal/mol
Surface area20020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.990, 67.430, 141.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 27937.707 Da / Num. of mol.: 2 / 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES 100mM pH7, PEG 8000, EDTA 10mM, CaCl2 10mM, Sodium Azide 0.006% Protein 10mg/mL
PH range: 5.5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54179 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.03→48.75 Å / Num. all: 40623 / Num. obs: 37957 / % possible obs: 98.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.2
Reflection shellResolution: 2.034→2.087 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata processing
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LYX

1lyx


Resolution: 2.03→48.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.819 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2329 1994 5 %RANDOM
Rwork0.1796 ---
obs0.18225 37956 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.988 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.03→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 62 326 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193917
X-RAY DIFFRACTIONr_bond_other_d0.0010.023727
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9535271
X-RAY DIFFRACTIONr_angle_other_deg0.913.0018543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.595490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.51325.46174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28915682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2621516
X-RAY DIFFRACTIONr_chiral_restr0.1250.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024439
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02877
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: 2.034→2.087 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 145 -
Rwork0.258 2515 -
obs--90.63 %

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