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- PDB-2v5b: The monomerization of Triosephosphate Isomerase from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 2v5b
TitleThe monomerization of Triosephosphate Isomerase from Trypanosoma cruzi
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / TIM / UNFOLDING / MONOTCTIM / GLYCOSOME / GLUCONEOGENESIS / LIPID SYNTHESIS / MONOMERIC MUTANT / GLYCOLYSIS / PENTOSE SHUNT / MONOMERIZATION / FATTY ACID BIOSYNTHESIS / TRIOSEPHOSPHATE ISOMERASE
Function / homology
Function and homology information


glycosome / 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 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsArreola, R. / Torres-Larios, A.
CitationJournal: Prog.Nucleic Acid Res. Mol.Biol. / Year: 2008
Title: The Monomerization of Triosephosphate Isomerase from Trypanosoma Cruzi.
Authors: Zarate-Perez, F. / Chanez-Cardenas, M.E. / Arreola, R. / Torres-Larios, A. / Vazquez-Contreras, E.
History
DepositionOct 2, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)26,5141
Polymers26,5141
Non-polymers00
Water97354
1
A: TRIOSEPHOSPHATE ISOMERASE

A: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,0292
Polymers53,0292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1860 Å2
ΔGint-11.3 kcal/mol
Surface area23370 Å2
MethodPQS
2


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.327, 77.673, 43.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE BIOLOGICAL UNIT CORRESPOND A MONOMER OF ASYMMETRIC UNIT. THE CRYSTALLOGRAFIC DIMER IS A CRYSTALLIZATION ARTIFACT MEDIATED BY A DISULFIDE BRIDGE OF CYS15 OF EACH MONOMER. THE SIZE EXCLUSION CHROMATOGRAPHY EXPERIMENTS DO NOT SHOW EVIDENCE OF A DIMER POPULATION.

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26514.391 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-68,84-251
Source method: isolated from a genetically manipulated source
Details: CYS A 118 IS A S-HYDROXYCYSTEINE / Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P52270, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 69 TO 83 (SEQUENCE: ITRSGAFTGEVSLQI) WERE SUBSTITUTED BY RESIDUES 76 TO 83 (SEQUENCE: GNADALAS)

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 282 K / Method: vapor diffusion / pH: 7.5
Details: CRYSTALS WERE GROWN AT 9 DEGREES. RESERVOIR SOLUTION OF 100 MM HEPES, PH 7.5, 10% PEG 6000, AND 5% 2-METHYL-2,4-PENTANEDIOL. THE CRYSTALS WERE CRYOPROTECTED BY ADDING PEG 400 30% TO THE ...Details: CRYSTALS WERE GROWN AT 9 DEGREES. RESERVOIR SOLUTION OF 100 MM HEPES, PH 7.5, 10% PEG 6000, AND 5% 2-METHYL-2,4-PENTANEDIOL. THE CRYSTALS WERE CRYOPROTECTED BY ADDING PEG 400 30% TO THE RESERVOIR. THEY WERE IMMEDIATELY FROZEN IN LIQUID NITROGEN.

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→52.13 Å / Num. obs: 16558 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 4.15 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.71
Reflection shellResolution: 2→2.02 Å / Redundancy: 4.21 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3.89 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERPROGRAM OF CCP4 6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCD

1tcd


Resolution: 2→52.13 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.198 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 16-20 ARE DISORDERED. RESIDUE CYS15 HAS A DISULFIDE BRIDGE WITH A CYS15 FROM A CRYSTALLOGRAPHIC NEIGHBOR FORMING A ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 16-20 ARE DISORDERED. RESIDUE CYS15 HAS A DISULFIDE BRIDGE WITH A CYS15 FROM A CRYSTALLOGRAPHIC NEIGHBOR FORMING A CRYSTALLOGRAPHIC DIMER. DISORDERED REGIONS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25693 835 5.1 %RANDOM
Rwork0.21157 ---
obs0.2137 15686 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.952 Å2
Baniso -1Baniso -2Baniso -3
1-2.08 Å20 Å20 Å2
2---2.56 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1809 0 0 54 1863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221862
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9452534
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.6855.083240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.79623.76677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.79315305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3871513
X-RAY DIFFRACTIONr_chiral_restr0.1260.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021395
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.2907
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21295
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1020.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3761.51219
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.37521906
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3143733
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.3944.5628
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.271 67
Rwork0.232 1133

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