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- PDB-1sux: CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ... -

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Basic information

Entry
Database: PDB / ID: 1sux
TitleCRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA CRUZI AND 3-(2-benzothiazolylthio)-1-propanesulfonic acid
ComponentsTriosephosphate isomerase, glycosomal
KeywordsISOMERASE / TRIOSEPHOSPHATE ISOMERASE / TRYPANOSOMA CRUZI / PROTEIN INTERFACES / BENZOTHIAZOLE INHIBITOR
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 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-(2-BENZOTHIAZOLYLTHIO)-1-PROPANESULFONIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTellez-Valencia, A. / Olivares-Illana, V. / Hernandez-Santoyo, A. / Perez-Montfort, R. / Costas, M. / Rodriguez-Romero, A. / Tuena De Gomez-Puyou, M. / Gomez-Puyou, A.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Inactivation of triosephosphate isomerase from Trypanosoma cruzi by an agent that perturbs its dimer interface.
Authors: Tellez-Valencia, A. / Olivares-Illana, V. / Hernandez-Santoyo, A. / Perez-Montfort, R. / Costas, M. / Rodriguez-Romero, A. / Lopez-Calahorra, F. / Tuena De Gomez-Puyou, M. / Gomez-Puyou, A.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Differences in the intersubunit contacts in triosephosphate isomerase from two closely related pathogenic trypanosomes
Authors: Maldonado, E. / Soriano-Garcia, M. / Moreno, A. / Cabrera, N. / Garza-Ramos, G. / De Gomez-Puyou, M. / Gomez-Puyou, A. / Perez-Montfort, R.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane
Authors: Gao, X.G. / Maldonado, E. / Perez-Monfort, R. / Garza-Ramos, G. / De Gomez-Puyou, M.T. / Gomez-Puyou, A. / Rodriguez-Romero, A.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)55,68310
Polymers54,7212
Non-polymers9628
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-104 kcal/mol
Surface area19440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.870, 75.580, 146.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Triosephosphate isomerase, glycosomal / TIM


Mass: 27360.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: MEXICAN NINOA STRAIN / Plasmid: PET23A / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL23(DE3) / References: UniProt: P52270, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BTS / 3-(2-BENZOTHIAZOLYLTHIO)-1-PROPANESULFONIC ACID


Mass: 289.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H11NO3S3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 43.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, HEPES, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 21, 2002 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 31622 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.04

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Processing

Software
NameVersionClassification
CNS1.1refinement
bioteXdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCD

1tcd


Resolution: 2→23.03 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1724206.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: FIVE DISCRETELY DISORDERED RESIDUES: GLU 19, GLU 27, LYS 53, SER 97 OF MONOMER A AND SER 2 0F MONOMER B. RESIDUE MET 1 OF BOTH CHAINS AND SIDE CHAINS FROM CG OF RESIDUES LYS A 157, LYS A ...Details: FIVE DISCRETELY DISORDERED RESIDUES: GLU 19, GLU 27, LYS 53, SER 97 OF MONOMER A AND SER 2 0F MONOMER B. RESIDUE MET 1 OF BOTH CHAINS AND SIDE CHAINS FROM CG OF RESIDUES LYS A 157, LYS A 177, GLN A 182 AND LYS B 218 HAVE WEAK ELECTRON DENSITY AND ARE NOT INCLUDED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2927 10 %RANDOM
Rwork0.183 ---
obs0.183 29330 88.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.7691 Å2 / ksol: 0.402909 e/Å3
Displacement parametersBiso mean: 19.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2--0.43 Å20 Å2
3----3.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å-0.01 Å
Refinement stepCycle: LAST / Resolution: 2→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3831 0 52 374 4257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.021.5
X-RAY DIFFRACTIONc_mcangle_it1.42
X-RAY DIFFRACTIONc_scbond_it1.742
X-RAY DIFFRACTIONc_scangle_it2.452.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.191 365 9.9 %
Rwork0.177 3325 -
obs-3325 68.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2SO4_XPLOR_PAR.PARAMSO4_XPLOR_PAR.TOP
X-RAY DIFFRACTION3BTS_PARB.PARAMBTS_PARB.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMWATER_REP.TOP

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