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- PDB-1tcd: TRYPANOSOMA CRUZI TRIOSEPHOSPHATE ISOMERASE -

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Basic information

Entry
Database: PDB / ID: 1tcd
TitleTRYPANOSOMA CRUZI TRIOSEPHOSPHATE ISOMERASE
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / INTRAMOLECULAR OXIDOREDUCTASE / GLYCOLYSIS / ISOMERIZATION BETWEEN GLYCERALDEHYDE 3-PHOSPHATE AND DIHYDROXYACETONE / ALPHA-BETA BARREL
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
Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMaldonado, E. / Soriano-Garcia, M. / Cabrera, N. / Garza-Ramos, G. / Tuena De Gomez-Puyou, M. / Gomez-Puyou, A. / Perez-Montfort, R.
Citation
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.
#1: Journal: Protein Pept.Lett. / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of Triosephosphate Isomerase from Trypanosoma Cruzi
Authors: Maldonado, E. / Moreno, A. / Pannerselvam, K. / Ostoa-Saloma, P. / Garza-Ramos, G. / Soriano-Garcia, M. / Perez-Montfort, R. / De Gomez-Puyou, M.T. / Gomez-Puyou, A.
History
DepositionJan 29, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)54,3162
Polymers54,3162
Non-polymers00
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-23 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.710, 77.650, 149.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.320858, 0.85768, 0.401792), (0.8282, 0.048262, 0.558351), (0.459495, 0.511915, -0.725815)
Vector: -47.59935, 5.71168, 63.86208)

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE / TIM


Mass: 27158.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: MEXICAN NINOA / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 (DE3) / References: UniProt: P52270, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.34 Å3/Da / Density % sol: 47.6 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.1 MNa-Hepes1reservoir
32 %(v/v)PEG4001reservoir
42.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Oct 2, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.83 Å / Num. obs: 42089 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 10
Reflection shellResolution: 1.83→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 3 / Rsym value: 0.105 / % possible all: 58.5
Reflection
*PLUS
Num. measured all: 132483
Reflection shell
*PLUS
% possible obs: 58.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
SAINT(SCALING ADAPTED FROM XSCALIBRE)data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 1.83→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3668 10.1 %RANDOM
Rwork0.191 ---
obs0.191 36414 82 %-
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.83→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 0 165 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.97
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.451.5
X-RAY DIFFRACTIONx_mcangle_it3.722
X-RAY DIFFRACTIONx_scbond_it6.932
X-RAY DIFFRACTIONx_scangle_it10.772.5
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 423 9.8 %
Rwork0.272 3877 -
obs--58.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor obs: 0.272

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