Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 61162.73 
• Atom Count: 4189 
• 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 typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
• Expression System: Escherichia coli


• 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 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, 1B9J, 1B5J, 1B5I, 1B58, 1B52, 1B51, 1B4Z, 1B46, 1B40, 1B3L, 1B3G, 1B3F, 1B32


• 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 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
• 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
• 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




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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
Molecule	Chains	Sequence Length	Organism	Details
PERIPLASMIC OLIGOPEPTIDE-BINDING PROTEIN	A	517	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)	Mutation(s): 0  Gene Names: oppA
Find proteins for P06202 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Go to UniProtKB:  P06202

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
PEPTIDE LYS-CYS-LYS	B	3	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.243 
• R-Value Work: 0.198 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 109.550	α = 90.00
b = 76.120	β = 90.00
c = 70.500	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance