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- PDB-5bmx: Crystal structure of T75N mutant of Triosephosphate isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 5bmx
TitleCrystal structure of T75N mutant of Triosephosphate isomerase from Plasmodium falciparum
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
Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBandyopadhyay, D. / Murthy, M.R.N. / Balaram, H. / Balaram, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology India
CitationJournal: Febs J. / Year: 2015
Title: Probing the role of highly conserved residues in triosephosphate isomerase - analysis of site specific mutants at positions 64 and 75 in the Plasmodial enzyme
Authors: Bandyopadhyay, D. / Murthy, M.R. / Balaram, H. / Balaram, P.
History
DepositionMay 24, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Other
Revision 1.3Oct 28, 2015Group: Database references
Revision 1.4Nov 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_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)113,01620
Polymers112,0434
Non-polymers97316
Water16,772931
1
A: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,50810
Polymers56,0212
Non-polymers4868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-20 kcal/mol
Surface area19020 Å2
MethodPISA
2
B: Triosephosphate isomerase
C: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,50810
Polymers56,0212
Non-polymers4868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-35 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.640, 106.720, 179.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28010.736 Da / Num. of mol.: 4 / Mutation: T75N, A163V
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 28% PEG 1450, 100mM Tris-HCl, 10mM Lithium sulphate, 0.5mM EDTA, 0.5mM DTT, 0.5mM sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2014
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.8→91.748 Å / Num. all: 88535 / Num. obs: 88535 / % possible obs: 97.2 % / Redundancy: 7.5 % / Rpim(I) all: 0.044 / Rrim(I) all: 0.124 / Rsym value: 0.116 / Net I/av σ(I): 4.014 / Net I/σ(I): 11.3 / Num. measured all: 668294
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.8-1.96.50.2972.580908123790.1190.2974.894.6
1.9-2.016.70.2143.380376119920.0870.2146.696.2
2.01-2.157.10.169480350113700.0670.1698.597.2
2.15-2.327.60.1424.680607106290.0550.14210.597.1
2.32-2.558.10.12957952098420.0480.1291297.6
2.55-2.858.30.1185.27465889710.0430.11813.798.2
2.85-3.298.40.1085.66720580100.040.10816.198.6
3.29-4.028.30.0995.85668168290.0370.09918.798.6
4.02-5.698.20.0925.74413354050.0340.09218.699
5.69-30.5837.70.0875.12385631080.0340.08716.798.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5X

1o5x


Resolution: 1.8→91.75 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.2231 / WRfactor Rwork: 0.1726 / FOM work R set: 0.8567 / SU B: 2.518 / SU ML: 0.079 / SU R Cruickshank DPI: 0.1292 / SU Rfree: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 4421 5 %RANDOM
Rwork0.167 ---
obs0.1694 84034 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.95 Å2 / Biso mean: 15.687 Å2 / Biso min: 4.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--0.26 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 1.8→91.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7636 0 56 931 8623
Biso mean--28.88 26.27 -
Num. residues----978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0197830
X-RAY DIFFRACTIONr_angle_refined_deg2.0121.94410582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1925972
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.37625.339369
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.635151369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9841532
X-RAY DIFFRACTIONr_chiral_restr0.1540.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025832
X-RAY DIFFRACTIONr_mcbond_it1.3881.3123906
X-RAY DIFFRACTIONr_mcangle_it1.9541.9584872
X-RAY DIFFRACTIONr_scbond_it2.4691.5583924
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 307 -
Rwork0.189 5912 -
all-6219 -
obs--93.32 %

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