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- PDB-2vfg: Crystal structure of the F96H mutant of Plasmodium falciparum tri... -

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Basic information

Entry
Database: PDB / ID: 2vfg
TitleCrystal structure of the F96H mutant of Plasmodium falciparum triosephosphate isomerase with 3-phosphoglycerate bound at the dimer interface
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / PLASMODIUM FALCIPARUM / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE / PENTOSE SHUNT / GLUCONEOGENESIS / LIPID SYNTHESIS / TIM / MUTANT / LOOP OPEN / 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
3-PHOSPHOGLYCERIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Biochemical and Structural Characterization of Residue 96 Mutants of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration and Identification of a Dimer- ...Title: Biochemical and Structural Characterization of Residue 96 Mutants of Plasmodium Falciparum Triosephosphate Isomerase: Active-Site Loop Conformation, Hydration and Identification of a Dimer-Interface Ligand-Binding Site.
Authors: Gayathri, P. / Banerjee, M. / Vijayalakshmi, A. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
History
DepositionNov 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED ... SHEET THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6998
Polymers111,9554
Non-polymers7444
Water12,196677
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3504
Polymers55,9772
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-29 kcal/mol
Surface area23520 Å2
MethodPQS
2
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3504
Polymers55,9772
Non-polymers3722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-28.5 kcal/mol
Surface area23280 Å2
MethodPQS
Unit cell
Length a, b, c (Å)90.197, 47.136, 109.167
Angle α, β, γ (deg.)90.00, 96.65, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.219814, -0.219974, 0.950417), (-0.224511, -0.959502, -0.170151), (0.949356, -0.175977, -0.260299)5.9527, 30.31604, -0.30488
2given(-0.985253, -0.0382, -0.166787), (-0.032088, 0.998717, -0.039186), (0.16807, -0.033256, -0.985214)91.25205, -19.8113, 44.32876
3given(-0.065818, -0.249381, -0.966166), (0.225769, -0.946877, 0.229022), (-0.971955, -0.203057, 0.118624)73.08436, 21.78019, 77.48316

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 27988.711 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Plasmid: PRC1008 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, triose-phosphate isomerase
#2: Chemical
ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 96 TO HIS ENGINEERED RESIDUE IN CHAIN A, ALA 163 TO VAL ...ENGINEERED RESIDUE IN CHAIN A, PHE 96 TO HIS ENGINEERED RESIDUE IN CHAIN A, ALA 163 TO VAL ENGINEERED RESIDUE IN CHAIN B, PHE 96 TO HIS ENGINEERED RESIDUE IN CHAIN B, ALA 163 TO VAL ENGINEERED RESIDUE IN CHAIN C, PHE 96 TO HIS ENGINEERED RESIDUE IN CHAIN C, ALA 163 TO VAL ENGINEERED RESIDUE IN CHAIN D, PHE 96 TO HIS ENGINEERED RESIDUE IN CHAIN D, ALA 163 TO VAL

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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: 2.09 Å3/Da / Density % sol: 41.2 % / Description: NONE
Crystal growpH: 5 / Details: 0.1 M SODIUM ACETATE PH 4.0-5.5, PEG 1450 8-24%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 14, 2006 / Details: OSMIC MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 62256 / % possible obs: 93.3 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.03 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.97 / % possible all: 82.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O5X

1o5x


Resolution: 1.95→23.78 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.568 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24819 2963 5.1 %RANDOM
Rwork0.20828 ---
obs0.21028 55242 87.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.326 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.95→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7705 0 44 677 8426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0227940
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8741.94710758
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.56751002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67725.374374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.559151404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9811532
X-RAY DIFFRACTIONr_chiral_restr0.0560.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025946
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1480.23909
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2890.25486
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2665
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.2123
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0620.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1661.55105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.29527974
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.27833208
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.4334.52774
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: 1.952→2.002 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 187
Rwork0.322 3228

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