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- PDB-8jbp: Crystal structure of triosephosphate isomerase from Leishmania or... -

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Basic information

Entry
Database: PDB / ID: 8jbp
TitleCrystal structure of triosephosphate isomerase from Leishmania orientalis at 1.45 angstroms resolution with an arsenic atom bound at Cys57
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / triosephosphate isomerase / TIM-barrel / dimer / an arsenic atom bound at Cys57
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / 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-type TIM barrel
Similarity search - Domain/homology
ARSENIC / Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania orientalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKuaprasert, B. / Leartsakulpanich, U. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Robinson, R.C. / Zhou, Y. / Mungthin, M. / Leelayoova, S. / Saehlee, S. / Choowongkomon, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Synchrotron Light Research Institute (SLRI)SLRI 3-62 and Kasetsart University Research and Development Institute, Kasetsart University, Thailand, Grant Number FF(KU) 6.64 Thailand
CitationJournal: To be published
Title: Leishmania orientalis triosephosphate isomerase crystal structure at 1.45 angstroms resolution and its potential specific inhibitors
Authors: Kuaprasert, B. / Leartsakulpanich, U. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Robinson, C.R. / Zhou, Y. / Mungthin, M. / Leelayoova, S. / Saehlee, S. / Kiriwan, D. / Choowongkomon, K.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6394
Polymers58,4892
Non-polymers1502
Water8,917495
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6394
Polymers58,4892
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3160 Å2
ΔGint-29 kcal/mol
Surface area19390 Å2
MethodPISA
2
B: Triosephosphate isomerase
hetero molecules

B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6394
Polymers58,4892
Non-polymers1502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3140 Å2
ΔGint-29 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.700, 79.353, 83.114
Angle α, β, γ (deg.)90.00, 101.24, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21A-595-

HOH

31A-612-

HOH

41B-556-

HOH

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Components

#1: Protein Triosephosphate isomerase


Mass: 29244.482 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania orientalis (eukaryote) / Gene: LSCM4_05371 / Plasmid: pET15b-LsTIM
Details (production host): lstim gene was ligated into pET15b at NdeI and BamHI sites
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A836H5J0, triose-phosphate isomerase
#2: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.29 Å3/Da / Density % sol: 46.22 % / Description: rod shape
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 5.7
Details: 18% PEG 8000 in 0.2M calcium acetate hydrate and 0.1M sodium cacodylate trihydrate pH5.9
PH range: 5.7 - 7.0 / Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Instrument Cryojet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 10, 2022 / Details: a pair of K-B mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 87903 / % possible obs: 98.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 10.69 Å2 / CC1/2: 0.979 / CC star: 0.995 / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.099 / Rrim(I) all: 0.247 / Χ2: 1.63 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.45-1.484.11.3165.343180.5170.8260.651.4720.44196.6
1.48-1.54.51.3342950.5750.8550.6351.4780.44697.1
1.5-1.534.91.35343520.5770.8560.6321.4980.46197.7
1.53-1.565.31.39743300.6140.8720.6321.5360.48497.9
1.56-1.65.71.33643880.7040.9090.5851.4610.49998.1
1.6-1.635.91.54643360.4980.8150.6681.6870.52298.2
1.63-1.675.91.4243820.5910.8620.621.5530.53798.6
1.67-1.725.81.14143940.6310.8790.5121.2540.59598.6
1.72-1.776.50.93143760.8010.9430.3841.0090.63498.7
1.77-1.836.40.7143810.8730.9650.2980.7710.7299
1.83-1.8960.54244510.8930.9710.240.5950.8799
1.89-1.976.60.38844130.9490.9870.1620.4211.12899.1
1.97-2.066.70.28243900.9650.9910.1150.3051.38799.3
2.06-2.176.60.21744270.9760.9940.090.2351.71399.4
2.17-2.36.30.18444280.9810.9950.0780.22.02499.2
2.3-2.486.30.14444500.9850.9960.0620.1572.32899.3
2.48-2.736.10.1244320.9890.9970.0530.1312.7899.5
2.73-3.125.70.09544390.9890.9970.0440.1053.76799.1
3.12-3.945.70.07644030.9920.9980.0350.0845.39497.8
3.94-506.40.06345180.9960.9990.0270.0694.6299

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-2000data scaling
DENZOdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.74 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.07 / SU ML: 0.04 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.064 / SU Rfree Cruickshank DPI: 0.0637
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19047 4421 5 %RANDOM
Rwork0.16215 ---
obs0.1636 83436 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.47 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.45→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3723 0 2 495 4220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123811
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163714
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.6365187
X-RAY DIFFRACTIONr_angle_other_deg0.5761.5668539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5525490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.296514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75610637
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
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_it1.3531.2791966
X-RAY DIFFRACTIONr_mcbond_other1.3491.2781966
X-RAY DIFFRACTIONr_mcangle_it1.9692.2862454
X-RAY DIFFRACTIONr_mcangle_other1.9692.2872455
X-RAY DIFFRACTIONr_scbond_it2.641.5451845
X-RAY DIFFRACTIONr_scbond_other2.6391.5461846
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9162.7042734
X-RAY DIFFRACTIONr_long_range_B_refined4.85214.74383
X-RAY DIFFRACTIONr_long_range_B_other4.712134244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.451→1.489 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 324 -
Rwork0.248 5952 -
obs--95.53 %

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