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- PDB-8j7c: Crystal structure of triosephosphate isomerase from Leishmania or... -

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Basic information

Entry
Database: PDB / ID: 8j7c
TitleCrystal structure of triosephosphate isomerase from Leishmania orientalis at 1.88A with an arsenic ion bound at Cys57
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / triosephosphate isomerase / TIM-barrel / dimer / an arsenic atom bound at Cys57
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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: 1.88 Å
AuthorsKuaprasert, B. / Attarataya, J. / Riangrungroj, P. / Pornthanakasem, W. / Suginta, W. / Mungthin, M. / Leelayoova, S. / Choowongkomon, K. / Leartsakulpanich, U.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Synchrotron Light Research Institute (SLRI) 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, R. / Zhou, Y. / Mungthin, M. / Leelayoova, S. / Saehlee, S. / Kiriwan, D. / Choowongkomon, K.
History
DepositionApr 27, 2023Deposition site: PDBJ / Processing site: PDBJ
SupersessionMay 1, 2024ID: 5CG7
Revision 1.0May 1, 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
Water8,845491
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 area3090 Å2
ΔGint-29 kcal/mol
Surface area19470 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_655-x+1,y,-z1
Buried area3090 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 76.450, 94.940
Angle α, β, γ (deg.)90.00, 101.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

21B-580-

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.: 491 / 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: 2.57 Å3/Da / Density % sol: 52.12 % / Description: rod shape
Crystal growTemperature: 291.15 K / Method: microbatch / pH: 5.9
Details: Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM ...Details: Equal volumes (1.0 microliter) of enzyme (24.2 mg/ml in 50 mM potassium phosphate buffer, pH 8.0, containing 50 mM KCl, 5 mM DTT, and 10% glycerol) and precipitant (PEG8000 18% w/v in 0.2 mM calcium acetate hydrate, 0.1 M and sodium cacodylate trihydrate, pH 5.9)
PH range: 5.9 - 6.5 / Temp details: Incubator

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 700 series Oxford Cryosystems / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLRI / Beamline: BL7.2W / Wavelength: 1.55 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2015 / Details: spherical mirror for CM and toroidal mirror for M
RadiationMonochromator: SI(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 1.88→21.56 Å / Num. obs: 46160 / % possible obs: 98.6 % / Redundancy: 2.8 % / Biso Wilson estimate: 6.92 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.059 / Rrim(I) all: 0.101 / Net I/av σ(I): 7.2 / Net I/σ(I): 11.9
Reflection shellResolution: 1.88→1.92 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2463 / CC1/2: 0.598 / Rpim(I) all: 0.399 / Rrim(I) all: 0.682 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
pointless1.8.8data scaling
MOSFLM7.0.9data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→19.98 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.038 / SU ML: 0.087 / Cross valid method: FREE R-VALUE / ESU R: 0.131 / ESU R Free: 0.128
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21377 2354 5.1 %RANDOM
Rwork0.17148 ---
obs0.17366 43811 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.047 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.88→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 2 491 4205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123830
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163728
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.6365220
X-RAY DIFFRACTIONr_angle_other_deg0.5171.5668576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0525496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.926514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95910640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024466
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
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_it1.3211.6481978
X-RAY DIFFRACTIONr_mcbond_other1.321.6481978
X-RAY DIFFRACTIONr_mcangle_it1.8812.952476
X-RAY DIFFRACTIONr_mcangle_other1.8812.9512477
X-RAY DIFFRACTIONr_scbond_it1.8971.8581852
X-RAY DIFFRACTIONr_scbond_other1.8971.861853
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9663.3262745
X-RAY DIFFRACTIONr_long_range_B_refined4.58418.754620
X-RAY DIFFRACTIONr_long_range_B_other4.32217.934444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.92 Å
RfactorNum. reflection% reflection
Rfree0.335 150 -
Rwork0.307 2921 -
obs--90.7 %

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