1TRD

THE INFLUENCE OF CRYSTAL PACKING ON CRYSTALLOGRAPHIC BINDING STUDIES: A NEW CRYSTAL FORM OF TRYPANOSOMAL TIM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Structures of the "open" and "closed" state of trypanosomal triosephosphate isomerase, as observed in a new crystal form: implications for the reaction mechanism.

Noble, M.E.Zeelen, J.P.Wierenga, R.K.

(1993) Proteins 16: 311-326

  • DOI: https://doi.org/10.1002/prot.340160402
  • Primary Citation of Related Structures:  
    1TPD, 1TRD, 2V5L

  • PubMed Abstract: 

    The structure of trypanosomal triosephosphate isomerase (TIM) has been solved at a resolution of 2.1A in a new crystal form grown at pH 8.8 from PEG6000. In this new crystal form (space group C2, cell dimensions 94.8 A, 48.3 A, 131.0 A, 90.0 degrees, 100.3 degrees, 90.0 degrees), TIM is present in a ligand-free state. The asymmetric unit consists of two TIM subunits. Each of these subunits is part of a dimer which is sitting on a crystallographic twofold axis, such that the crystal packing is formed from two TIM dimers in two distinct environments. The two constituent monomers of a given dimer are, therefore, crystallographically equivalent. In the ligand-free state of TIM in this crystal form, the two types of dimer are very similar in structure, with the flexible loops in the "open" conformation. For one dimer (termed molecule-1), the flexible loop (loop-6) is involved in crystal contacts. Crystals of this type have been used in soaking experiments with 0.4 M ammonium sulphate (studied at 2.4 A resolution), and with 40 microM phosphoglycolohydroxamate (studied at 2.5 A resolution). It is found that transfer to 0.4 M ammonium sulphate (equal to 80 times the Ki of sulphate for TIM), gives rise to significant sulphate binding at the active site of one dimer (termed molecule-2), and less significant binding at the active site of the other. In neither dimer does sulphate induce a "closed" conformation. In a mother liquor containing 40 microM phosphoglycolohydroxamate (equal to 10 times the Ki of phosphoglycolohydroxamate for TIM), an inhibitor molecule binds at the active site of only that dimer of which the flexible loop is free from crystal contacts (molecule-2). In this dimer, it induces a closed conformation. These three structures are compared and discussed with respect to the mode of binding of ligand in the active site as well as with respect to the conformational changes resulting from ligand binding.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRIOSEPHOSPHATE ISOMERASE
A, B
250Trypanosoma brucei bruceiMutation(s): 0 
EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei)
Explore P04789 
Go to UniProtKB:  P04789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04789
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download Ideal Coordinates CCD File 
C [auth B]PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PGH Binding MOAD:  1TRD Ki: 4000 (nM) from 1 assay(s)
PDBBind:  1TRD Ki: 4000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.62α = 90
b = 48β = 100.33
c = 131.31γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-02-14
    Changes: Data collection, Database references, Derived calculations