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- PDB-2oma: Crystallographic analysis of a chemically modified triosephosphat... -

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Basic information

Entry
Database: PDB / ID: 2oma
TitleCrystallographic analysis of a chemically modified triosephosphate isomerase from Trypanosoma cruzi with dithiobenzylamine (DTBA)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / Triosephosphate isomerase / Trypanosoma cruzi / protein interfaces / dithiobisbenzylamine
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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsRodriguez-Romero, A. / Gomez-Puyou, A.
Citation
Journal: PLoS Negl Trop Dis / Year: 2007
Title: Perturbation of the Dimer Interface of Triosephosphate Isomerase and its Effect on Trypanosoma cruzi.
Authors: Olivares-Illana, V. / Rodriguez-Romero, A. / Becker, I. / Berzunza, M. / Garcia, J. / Perez-Montfort, R. / Cabrera, N. / Lopez-Calahorra, F. / de Gomez-Puyou, M.T. / Gomez-Puyou, A.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Inactivation of triosephosphate isomerase from trypanosoma cruzi by an agent 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.
History
DepositionJan 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.2Aug 30, 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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)56,03815
Polymers54,7052
Non-polymers1,33313
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-124 kcal/mol
Surface area19940 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.206, 75.337, 146.427
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose- phosphate isomerase


Mass: 27352.418 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 / 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.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 43.65 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 5 MICROL OF THE PROTEIN SOLUTION WERE MIXED WITH 5 MICROL OF 2 % POLYETHYLENE GLYCOL 400, 0.1 M HEPES, 2.0M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 7.50. ...Details: 5 MICROL OF THE PROTEIN SOLUTION WERE MIXED WITH 5 MICROL OF 2 % POLYETHYLENE GLYCOL 400, 0.1 M HEPES, 2.0M AMMONIUM SULFATE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, PH 7.50. CRYSTAL SOAKED IN DITHIOBENZYLAMINE

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 3, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→41.45 Å / Num. obs: 23141 / % possible obs: 91 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 10.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.8 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCD

1tcd


Resolution: 2.15→41.45 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.324 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.363 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMS ARE ASSIGNED REDUCED OCCUPANCIES WHEN ELECTRON DENSITY IS WEAK OR ATOMS HAVE PARTIAL OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1248 5.1 %RANDOM
Rwork0.196 ---
obs0.199 23141 91 %-
all-25429 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.788 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.15→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3846 0 76 267 4189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224002
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9141.9655431
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.224.096166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88115662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4241526
X-RAY DIFFRACTIONr_chiral_restr0.1330.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022948
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.21977
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22637
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2450.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5881.52578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73324001
X-RAY DIFFRACTIONr_scbond_it3.09631654
X-RAY DIFFRACTIONr_scangle_it4.3424.51430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 76 -
Rwork0.213 1783 -
obs--96.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0382-0.0488-0.13420.36340.11990.48090.00630.01790.0241-0.04190.03020.0024-0.03310.0082-0.0365-0.00390.0136-0.0093-0.0180.0005-0.00543.6386-0.0798-4.8227
20.18050.1087-0.1450.14370.00030.2145-0.03070.0136-0.00660.022-0.0026-0.0457-0.0398-0.0660.0333-0.02370.0101-0.004-0.0124-0.0189-0.006313.3632-20.4982-31.7605
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2511 - 250
2X-RAY DIFFRACTION2BB2 - 2511 - 250

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