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- PDB-5tim: REFINED 1.83 ANGSTROMS STRUCTURE OF TRYPANOSOMAL TRIOSEPHOSPHATE ... -

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Basic information

Entry
Database: PDB / ID: 5tim
TitleREFINED 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
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glycerol catabolic process / glyceraldehyde-3-phosphate biosynthetic process / gluconeogenesis / glycolytic process / cytosol / cytoplasm
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.83 Å
AuthorsWierenga, R.K. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Refined 1.83 A structure of trypanosomal triosephosphate isomerase crystallized in the presence of 2.4 M-ammonium sulphate. A comparison with the structure of the trypanosomal triosephosphate ...Title: Refined 1.83 A 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. / Vriend, G. / Nauche, S. / Hol, W.G.
#1: 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.
#2: 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.M. / Wierenga, R.K. / Lambeir, A.-M. / Opperdoes, F.R. / Thunnissen, A.-M.W.H. / Kalk, K.H. / Groendijk, H. / Hol, W.G.J.
#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
SupersessionOct 15, 1992ID: 2TIM
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 6, 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

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0785
Polymers53,7322
Non-polymers3463
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-52 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.140, 97.690, 46.560
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 ALMOST CLOSED. THERE IS A SULFATE ION 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: took Wierenga et al.,(1984) from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
145 mg/mlprotein1drop
20.2 MMOPS1reservior
32.4 Mammonium sulphate1reservoir
41 mMdithiothreitol1reservoir
51 mMazide1reservoir
61 mMEDTA1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 1.83 Å / Lowest resolution: 25 Å / Num. obs: 38819 / Num. measured all: 122216 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.83→6 Å / Rfactor obs: 0.183
Refinement stepCycle: LAST / Resolution: 1.83→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 18 279 4063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg2.9
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_planes0.024
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 37568 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 2.9

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