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- PDB-1tri: THE CRYSTAL STRUCTURE OF AN ENGINEERED MONOMERIC TRIOSEPHOSPHATE ... -

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Basic information

Entry
Database: PDB / ID: 1tri
TitleTHE CRYSTAL STRUCTURE OF AN ENGINEERED MONOMERIC TRIOSEPHOSPHATE ISOMERASE, MONOTIM: THE CORRECT MODELLING OF AN EIGHT-RESIDUE LOOP
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
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 / cytoplasm / 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 brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsWierenga, R.K.
CitationJournal: Structure / Year: 1993
Title: The crystal structure of an engineered monomeric triosephosphate isomerase, monoTIM: the correct modelling of an eight-residue loop.
Authors: Borchert, T.V. / Abagyan, R. / Kishan, K.V. / Zeelen, J.P. / Wierenga, R.K.
History
DepositionOct 8, 1993Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1892
Polymers26,0931
Non-polymers961
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.780, 42.800, 68.840
Angle α, β, γ (deg.)90.00, 108.22, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26092.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TPIS_TRYBB SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ARG 203 ALA 203 THE DISCREPANCY IS DUE TO THE CORRECT IDENTIFICATION IN THE DEPOSITOR'S LABORATORY AFTER TPIS_TRYBB HAD BEEN SUBMITTED. (BORCHERT ET AL., EUR. J. BIOCHEM., V211, 703, 1993). THIS ALANINE IS COMPLETELY CONSERVED IN ALL PUBLISHED TIM SEQUENCES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.23 %
Crystal grow
*PLUS
Temperature: 12 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES1reservoir
2180 mM1reservoirLi2SO4
326 %PEG60001reservoir
45 mMdithiothreitol1reservoir
51 mMEDTA1reservoir
61 mM1reservoirNaN3

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 7368 / Num. measured all: 15495
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 29 %

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→32.6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.165 -
obs0.165 7368
Refinement stepCycle: LAST / Resolution: 2.4→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 5 21 1831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg2.61
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.165 / Rfactor Rwork: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.61

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