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- PDB-5bmw: Crystal structure of T75V mutant of Triosephosphate isomerase fro... -

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Basic information

Entry
Database: PDB / ID: 5bmw
TitleCrystal structure of T75V 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 / gluconeogenesis / glycolytic process / identical protein binding
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: 1.86 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 23, 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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)56,76914
Polymers55,9922
Non-polymers77812
Water8,701483
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-36 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.210, 76.020, 74.360
Angle α, β, γ (deg.)90.000, 97.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 27995.766 Da / Num. of mol.: 2 / Mutation: T75V, 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

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Non-polymers , 5 types, 495 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / 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.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 1.97 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 1450, 100 mM MES buffer, 10 mM Calcium chloride, 0.5 mM EDTA, 0.5 mM DTT, 0.5 mM sodium azide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2014
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.859→73.73 Å / Num. all: 36392 / Num. obs: 36392 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rpim(I) all: 0.025 / Rrim(I) all: 0.061 / Rsym value: 0.056 / Net I/av σ(I): 9.916 / Net I/σ(I): 22.2 / Num. measured all: 203849
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.86-1.965.20.1564.72704252110.0750.1569.898.4
1.96-2.085.50.10272767450090.0470.10214.4100
2.08-2.225.60.07892629947080.0360.07817.8100
2.22-2.45.60.0699.92481144060.0320.06920.9100
2.4-2.635.70.05911.32311140530.0270.05922.9100
2.63-2.945.70.04913.42097036650.0220.04926.2100
2.94-3.395.80.04214.71870432390.0190.04231.1100
3.39-4.165.80.04413.51592927430.020.04436.3100
4.16-5.885.80.042131251321520.0190.04237.4100
5.88-38.8775.60.0413.3679612060.0180.043399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.16data scaling
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5X

1o5x


Resolution: 1.86→73.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1829 / WRfactor Rwork: 0.1316 / FOM work R set: 0.9111 / SU B: 2.335 / SU ML: 0.071 / SU R Cruickshank DPI: 0.1271 / SU Rfree: 0.1234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1824 1816 5 %RANDOM
Rwork0.1314 ---
obs0.134 34547 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 46.58 Å2 / Biso mean: 11.586 Å2 / Biso min: 4.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å2-0 Å2-0.02 Å2
2---0.16 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.86→73.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 47 483 4389
Biso mean--15.75 23.63 -
Num. residues----493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193985
X-RAY DIFFRACTIONr_bond_other_d0.0020.023814
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9495381
X-RAY DIFFRACTIONr_angle_other_deg1.03338763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94425.426188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75815705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2581516
X-RAY DIFFRACTIONr_chiral_restr0.1110.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024532
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02910
X-RAY DIFFRACTIONr_mcbond_it0.8960.9771978
X-RAY DIFFRACTIONr_mcbond_other0.890.9771977
X-RAY DIFFRACTIONr_mcangle_it1.3031.462471
LS refinement shellResolution: 1.859→1.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 140 -
Rwork0.197 2436 -
all-2576 -
obs--96.81 %

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