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- PDB-1tsi: STRUCTURE OF THE COMPLEX BETWEEN TRYPANOSOMAL TRIOSEPHOSPHATE ISO... -

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Basic information

Entry
Database: PDB / ID: 1tsi
TitleSTRUCTURE OF THE COMPLEX BETWEEN TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE AND N-HYDROXY-4-PHOSPHONO-BUTANAMIDE: BINDING AT THE ACTIVE SITE DESPITE AN "OPEN" FLEXIBLE 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
N-HYDROXY-4-PHOSPHONO-BUTANAMIDE / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.84 Å
AuthorsVerlinde, C.L.M.J.
Citation
Journal: Protein Sci. / Year: 1992
Title: Structure of the complex between trypanosomal triosephosphate isomerase and N-hydroxy-4-phosphono-butanamide: binding at the active site despite an "open" flexible loop conformation.
Authors: Verlinde, C.L. / Witmans, C.J. / Pijning, T. / Kalk, K.H. / Hol, W.G. / Callens, M. / Opperdoes, F.R.
#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: 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.
#3: 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
DepositionNov 19, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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)54,0853
Polymers53,9042
Non-polymers1811
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-22 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.340, 97.150, 46.450
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*. THE CRYSTALS USED FOR THIS STRUCTURE DETERMINATION WERE GROWN IN THE PRESENCE OF 2.4M AMMONIUM SULFATE (SEE PROTEIN DATA BANK ENTRY 2TIM), BUT BEFORE DATA COLLECTION THESE CRYSTALS WERE TRANSFERRED TO A MOTHER LIQUOR WITHOUT SULFATE. THE ACTIVE SITE OF SUBUNIT *A* CONTAINS THE INHIBITOR N-HYDROXY-4-PHOSPHONO-BUTANAMIDE (KI = 0.3 * 10**-3 M). IN THIS ENTRY THE FLEXIBLE LOOP (LOOP 6) OF EACH SUBUNIT IS IN AN OPEN CONFORMATION.

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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: Chemical ChemComp-4PB / N-HYDROXY-4-PHOSPHONO-BUTANAMIDE


Mass: 181.084 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
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
30.2 M3-(N-morpholino)-propane-sulphonic acid1drop
41 mMEDTA1drop
51 mMdithiothreitol1drop
61 mMsodium azide1drop
760 %ammonium sulphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.84 Å / Num. obs: 6530 / % possible obs: 95.8 % / Rmerge(I) obs: 0.063

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.84→6 Å / σ(F): 0 /
RfactorNum. reflection
obs0.115 6530
Refinement stepCycle: LAST / Resolution: 2.84→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3771 0 11 53 3835
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg3.2
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: 0.115
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 3.5 Å2
Refine LS restraints
*PLUS
Type: t_angle_d / Dev ideal: 3.2

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