Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.16 kDa 
• Atom Count: 4377 
• Residue Count: 520 
• Unique protein chains: 2

1B05

Structure of oligo-peptide binding protein complexed with LYS-CYS-LYS

• DOI: 10.2210/pdb1B05/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-11-20 Released: 1998-11-25 
• Deposition Author(s): Tame, J.R.H., Wilkinson, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.198 

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

• PubMed: 10438628 
• DOI: 10.1006/jmbi.1999.2929
• Primary Citation of Related Structures:  
  1QKB, 1QKA, 1B05, 1B32, 1B46, 1B3G, 1B3F, 1B40, 1B3L, 1B4Z


• 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 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.

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Related Citations: 

• 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 Biol 3: 998

• 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 D Biol Crystallogr 51: 39

• 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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN	A	517	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: oppA
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P06202  Go to UniProtKB:  P06202

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE LYS-CYS-LYS	B	3	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
U1	A	URANIUM ATOM U JFALSRSLKYAFGM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.55	α = 90
b = 76.12	β = 90
c = 70.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
CCP4	model building
REFMAC	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-11-20 
• Released Date: 1998-11-25 
Deposition Author(s): Tame, J.R.H., Wilkinson, A.J.

Revision History 

• Version 1.0: 1998-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance