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- PDB-4tim: CRYSTALLOGRAPHIC AND MOLECULAR MODELING STUDIES ON TRYPANOSOMAL T... -

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Basic information

Entry
Database: PDB / ID: 4tim
TitleCRYSTALLOGRAPHIC AND MOLECULAR MODELING STUDIES ON TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE: A CRITICAL ASSESSMENT OF THE PREDICTED AND OBSERVED STRUCTURES OF THE COMPLEX WITH 2-PHOSPHOGLYCERATE
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 / 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-PHOSPHOGLYCERIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsNobel, M.E.M. / Wierenga, R.K. / Hol, W.G.J.
Citation
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. / Verlinde, C.L. / Groendijk, H. / Kalk, K.H. / Wierenga, R.K. / Hol, W.G.
#1: 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.
#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.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.
#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 11, 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 1.3Feb 28, 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)53,9183
Polymers53,7322
Non-polymers1861
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-25 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.590, 97.290, 46.700
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*.

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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-2PG / 2-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: THE CRYSTALS USED FOR THIS STRUCTURE DETERMINATION WERE GROWN IN THE PRESENCE OF 2.4M AMMONIUM SULFATE (SEE PROTEIN DATA BANK ENTRIES 2TIM AND 5TIM), BUT BEFORE DATA COLLECTION THESE ...Details: THE CRYSTALS USED FOR THIS STRUCTURE DETERMINATION WERE GROWN IN THE PRESENCE OF 2.4M AMMONIUM SULFATE (SEE PROTEIN DATA BANK ENTRIES 2TIM AND 5TIM), BUT BEFORE DATA COLLECTION THESE CRYSTALS WERE TRANSFERRED TO A MOTHER LIQUOR WITHOUT SULFATE CONTAINING 30MM 2-PHOSPHOGLYCERATE. THE ACTIVE SITE OF CHAIN *A* ("OPEN"-CONFORMATION) HAS NO BOUND 2-PHOSPHOGLYCERATE. THE ACTIVE SITE OF CHAIN *B* ("CLOSED"-CONFORMATION) HAS A BOUND 2-PHOSPHOGLYCERATE.
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: took 19 from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mlprotein1drop
22.4 Mammonium sulfate1drop
30.2 MMOPS1drop
41 mMdithiothreitol1reservoir
51 mMsodium azide1reservoir
61 mMEDTA1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 15 Å / Num. all: 17456 / % possible obs: 84.1 % / Rmerge(I) obs: 0.058

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.4→15 Å /
RfactorNum. reflection
obs0.149 17456
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 11 130 3907
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.013
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg2.3

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