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- PDB-3tim: THE CRYSTAL STRUCTURE OF THE "OPEN" AND THE "CLOSED" CONFORMATION... -

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Basic information

Entry
Database: PDB / ID: 3tim
TitleTHE CRYSTAL STRUCTURE OF THE "OPEN" AND THE "CLOSED" CONFORMATION OF THE FLEXIBLE LOOP OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE
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: 2.8 Å
AuthorsWierenga, R.K.
Citation
Journal: Proteins / Year: 1991
Title: The crystal structure of the "open" and the "closed" conformation of the flexible loop of trypanosomal triosephosphate isomerase.
Authors: Wierenga, R.K. / Noble, M.E. / Postma, J.P. / Groendijk, H. / Kalk, K.H. / Hol, W.G. / Opperdoes, F.R.
#1: Journal: J.Mol.Biol. / Year: 1987
Title: Structure Determination of the Glycosomal Triosephosphate Isomerase from Trypanosoma Brucei Brucei at 2.4 Angstroms Resolution
Authors: Wierenga, R.K. / Kalk, K.H. / Hol, W.G.J.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Preliminary Crystallographic Studies of Triosephosphate Isomerase from the Blood Parasite Trypanosoma Brucei Brucei
Authors: Wierenga, R.K. / Hol, W.G.J. / Misset, O. / Opperdoes, F.R.
History
DepositionMay 15, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *A* AND *B* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA- ...SHEET THE SHEETS PRESENTED AS *A* AND *B* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS 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
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,9042
Polymers53,9042
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-21 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.140, 96.480, 46.430
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 TRIOSEPHOSPHATE ISOMERASE


Mass: 26951.947 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE SPECIFICATIONS WERE MADE BY USE OF PROGRAM *DSSP* OF W. KABSCH AND C. SANDER.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal grow
*PLUS
pH: 7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 MMOPS1reservoir
21 mMEDTA1reservoir
31 mMsodium azide1reservoir
41 mMdithiothreitol1reservoir
52.4 Mammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 10369 / % possible obs: 80 % / Num. measured all: 26975 / Rmerge(I) obs: 0.065

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.8→6 Å / Rfactor obs: 0.139
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 0 30 3808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Rfactor obs: 0.139
Solvent computation
*PLUS
Displacement parameters
*PLUS

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