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- PDB-1ci1: CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA C... -

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Basic information

Entry
Database: PDB / ID: 1ci1
TitleCRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM TRYPANOSOMA CRUZI IN HEXANE
ComponentsPROTEIN (TRIOSEPHOSPHATE ISOMERASE)
KeywordsTRIOSEPHOSPHATE ISOMERASE / TRYPANOSOMA CRUZI / ORGANIC SOLVENT / HEXANE / OLIGOMERIC PROTEIN
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
HEXANE / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2 Å
AuthorsGao, X.-G. / Maldondo, E. / Perez-Montfort, R. / De Gomez-Puyou, M.T. / Gomez-Puyou, A. / Rodriguez-Romero, A.
Citation
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-Montfort, R. / Garza-Ramos, G. / de Gomez-Puyou, M.T. / Gomez-Puyou, A. / Rodriguez-Romero, 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.
History
DepositionApr 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (TRIOSEPHOSPHATE ISOMERASE)
B: PROTEIN (TRIOSEPHOSPHATE ISOMERASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9795
Polymers54,7212
Non-polymers2593
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-11 kcal/mol
Surface area19380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.656, 77.650, 149.211
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 PROTEIN (TRIOSEPHOSPHATE ISOMERASE) / 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-HEX / HEXANE


Mass: 86.175 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 3 N-TERMINAL RESIDUE WERE NOT BUILT INTO THE MODEL A AS THEY WERE NOT SEEEN IN THE ...THE FIRST 3 N-TERMINAL RESIDUE WERE NOT BUILT INTO THE MODEL A AS THEY WERE NOT SEEEN IN THE DENSITY MAPS THE FIRST 2 N-TERMINAL RESIDUE WERE NOT BUILT INTO THE MODEL B AS THEY WERE NOT SEEN IN THE DENSITY MAPS

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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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: PROTEIN WAS CRYSTALLIZED AT ROOM TEMPERATUTE BY VAPER DIFFUSION FROM 0.1 M NA HEPES PH7.5, 2%(V/V) PEG400 AND 2.0 M AMMONIUM SULFATE, THEN SOAKED IN ANHYDROUS N-HEXANE. , VAPOR DIFFUSION
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MHEPES1reservoir
22 %(v/v)PEG4001reservoir
32.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 21, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 31766 / % possible obs: 84.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.116 / Net I/σ(I): 4.64
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 2.1 / % possible all: 65.5
Reflection
*PLUS
Num. measured all: 172135

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Processing

Software
NameVersionClassification
X-PLOR3.851(ONLINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER
Starting model: PDB ENTRY 1TCD

1tcd


Resolution: 2→5 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2696 10 %RANDOM
Rwork0.181 ---
obs-26956 82.4 %-
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 18 236 4072
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.561.5
X-RAY DIFFRACTIONx_mcangle_it2.212
X-RAY DIFFRACTIONx_scbond_it32
X-RAY DIFFRACTIONx_scangle_it4.582.5
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 350 9.9 %
Rwork0.309 3197 -
obs--65.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.HEXTOP.HEX
X-RAY DIFFRACTION3TOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 5 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.64
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.309

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