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- PDB-6tim: THE ADAPTABILITY OF THE ACTIVE SITE OF TRYPANOSOMAL TRIOSEPHOSPHA... -

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Basic information

Entry
Database: PDB / ID: 6tim
TitleTHE ADAPTABILITY OF THE ACTIVE SITE OF TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE AS OBSERVED IN THE CRYSTAL STRUCTURES OF THREE DIFFERENT COMPLEXES
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
SN-GLYCEROL-3-PHOSPHATE / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsNoble, M.E.M. / Wierenga, R.K. / Hol, W.G.J.
Citation
Journal: Proteins / Year: 1991
Title: The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes.
Authors: Noble, M.E. / Wierenga, R.K. / Lambeir, A.M. / Opperdoes, F.R. / Thunnissen, A.M. / Kalk, K.H. / Groendijk, H. / Hol, W.G.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Refined 1.83 Angstroms Structure of Trypanosomal Triosephosphate Isomerase Crystallized in the Presence of 2.4 M-Ammonium Sulphate. A Comparison with the Structure of the Trypanosomal ...Title: Refined 1.83 Angstroms Structure of Trypanosomal Triosephosphate Isomerase Crystallized in the Presence of 2.4 M-Ammonium Sulphate. A Comparison with the Structure of the Trypanosomal Triosephosphate Isomerase-Glycerol-3-Phosphate Complex
Authors: Wierenga, R.K. / Noble, M.E.M. / Vriend, G. / Nauche, S. / Hol, W.G.J.
#2: 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.M. / Postma, J.P.M. / Groendijk, H. / Kalk, K.H. / Hol, W.G.J. / Opperdoes, F.R.
#3: Journal: J.Med.Chem. / Year: 1991
Title: Crystallographic and Molecular Modeling Studies on Trypanosomal Triosephosphate Isomerase: A Critical Assessment of the Predicted and Observed Structures of the Complex with 2-Phosphoglycerate
Authors: Noble, M.E.M. / Verlinde, C.L.M.J. / Groendijk, H. / Kalk, K.H. / Wierenga, R.K. / Hol, W.G.J.
#4: 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.
#5: 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
DepositionApr 23, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9043
Polymers53,7322
Non-polymers1721
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.360, 97.590, 46.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONSISTS OF A DIMER. THE TWO MOLECULES HAVE BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*. SUBUNITS *A* AND *B* DO NOT HAVE IDENTICAL CONFORMATIONS. THE FLEXIBLE LOOP OF SUBUNIT *A* IS OPEN AND THE FLEXIBLE LOOP OF SUBUNIT *B* IS CLOSED. GLYCEROL-3-PHOSPHATE IS BOUND IN THE ACTIVE SITE OF SUBUNIT *B*.

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26865.832 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: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growDetails: THIS STRUCTURE IS OBTAINED FROM CRYSTALS GROWN IN 2.4M AMMONIUM SULPHATE AND TRANSFERRED INTO SULPHATE FREE MOTHER LIQUOR CONTAINING 6MM DL-GLYCEROL-3-PHOSPHATE.
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.5 mg/mltriosephosphate isomerase1drop0.9 M ammonium sulphate
260 %ammonium sulfate1drop
31 mMEDTA1drop
40.2 M3-(N-morpholino)-propane-sulphonic acid1drop
51 mMdithiothreitol1drop
61 mMsodium azide1drop
760 %ammonium sulphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 18064 / Rmerge(I) obs: 0.043

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.2→50 Å /
RfactorNum. reflection
obs0.37 16881
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 10 91 3867
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.5
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.023
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. reflection obs: 16881 / Rfactor obs: 0.137
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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