1B58

OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KYK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic and calorimetric analysis of peptide binding to OppA protein.

Sleigh, S.H.Seavers, P.R.Wilkinson, A.J.Ladbury, J.E.Tame, J.R.

(1999) J.Mol.Biol. 291: 393-415

  • DOI: 10.1006/jmbi.1999.2929
  • Primary Citation of Related Structures:  1B05, 1B32, 1B3F, 1B3G, 1B3L, 1B40, 1B46, 1B4Z, 1B51, 1B52, 1B5I, 1B5J, 1B9J, 1QKA, 1QKB

  • PubMed Abstract: 
  • Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the olig ...

    Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.


    Related Citations: 
    • The Structural Basis of Sequence-Independent Peptide Binding by Oppa Protein
      Tame, J.R.H.,Murshudov, G.N.,Dodson, E.J.,Neil, T.K.,Dodson, G.G.,Higgins, C.F.,Wilkinson, A.J.
      (1994) Science 264: 1578
    • The Crystal Structures of the Oligopeptide-Binding Protein Oppa Complexed with Tripeptide and Tetrapeptide Ligands
      Tame, J.R.H.,Dodson, E.J.,Murshudov, G.,Higgins, C.F.,Wilkinson, A.J.
      (1995) Structure 3: 1395
    • Structure Determination of Oppa at 2.3 Angstroms Resolution Using Multiple Wavelength Anomalous Methods
      Glover, I.D.,Denny, R.,Nguti, N.D.,Mcsweeney, S.,Thompson, A.,Dodson, E.,Wilkinson, A.J.,Tame, J.R.H.
      (1995) Acta Crystallogr.,Sect.D 51: 39
    • The Role of Water in Sequence-Independent Ligand Binding by an Oligopeptide Transporter Protein
      Tame, J.R.H.,Sleigh, S.H.,Wilkinson, A.J.,Ladbury, J.E.
      (1996) Nat.Struct.Mol.Biol. 3: 998


    Organizational Affiliation

    Structural Biology Centre Department of Chemistry, University of York, York, YO10 5DD, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (OLIGO-PEPTIDE BINDING PROTEIN)
A
517Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Gene Names: oppA
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P06202
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (LYS-TYR-LYS)
B
3N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUM
Query on IUM

Download SDF File 
Download CCD File 
A
URANYL (VI) ION
O2 U
IZLHQJIUOZHTLW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 110.670α = 90.00
b = 76.620β = 90.00
c = 71.650γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CCP4model building
CCP4phasing
DENZOdata reduction
CCP4data scaling
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance