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- PDB-3pvf: Structure of C126S mutant of Plasmodium falciparum triosephosphat... -

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Basic information

Entry
Database: PDB / ID: 3pvf
TitleStructure of C126S mutant of Plasmodium falciparum triosephosphate isomerase complexed with PGA
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Tim barrel
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: 1.73 Å
AuthorsSamanta, M. / Banerjee, M. / Murthy, M.R.N. / Balaram, H. / Balaram, P.
CitationJournal: Febs J. / Year: 2011
Title: Probing the role of the fully conserved Cys126 in triosephosphate isomerase by site-specific mutagenesis--distal effects on dimer stability.
Authors: Samanta, M. / Banerjee, M. / Murthy, M.R. / Balaram, H. / Balaram, P.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 28, 2013Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)28,1382
Polymers27,9821
Non-polymers1561
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2754
Polymers55,9632
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3280 Å2
ΔGint-24 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.510, 63.100, 53.200
Angle α, β, γ (deg.)90.00, 117.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 27981.674 Da / Num. of mol.: 1 / Mutation: C126S
Source method: isolated from a genetically manipulated source
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG, HEPES buffer(pH 7.5), 10mM Lithium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 30, 2009 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.73→38.91 Å / Num. obs: 25341 / % possible obs: 93.94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.13 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 17.37
Reflection shellResolution: 1.732→1.777 Å / Rmerge(I) obs: 0.125 / % possible all: 83.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LYX

1lyx


Resolution: 1.73→26.25 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.991 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19416 1283 5.1 %RANDOM
Rwork0.15193 ---
obs0.15416 24058 94.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.673 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 9 343 2307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222042
X-RAY DIFFRACTIONr_angle_refined_deg2.061.952765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3015257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.19825.784102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.21215377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.729158
X-RAY DIFFRACTIONr_chiral_restr0.160.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021544
X-RAY DIFFRACTIONr_mcbond_it1.2321.51247
X-RAY DIFFRACTIONr_mcangle_it1.99722029
X-RAY DIFFRACTIONr_scbond_it3.3863795
X-RAY DIFFRACTIONr_scangle_it5.2864.5733
LS refinement shellResolution: 1.732→1.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 77 -
Rwork0.37 1553 -
obs-6534 83.21 %

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