3RYB | pdb_00003ryb

Lactococcal OppA complexed with SLSQSLSQS

• PDB DOI: https://doi.org/10.2210/pdb3RYB/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Lactococcus cremoris subsp. cremoris MG1363
• Expression System: Lactococcus cremoris subsp. cremoris MG1363
• Mutation(s): No 


• Deposited: 2011-05-11 Released: 2011-06-29 
• Deposition Author(s): Berntsson, R.P.-A., Thunnissen, A.-M.W.H., Poolman, B., Slotboom, D.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Importance of a Hydrophobic Pocket for Peptide Binding in Lactococcal OppA.

Berntsson, R.P., Thunnissen, A.M., Poolman, B., Slotboom, D.J.

(2011) J Bacteriol 193: 4254-4256

• PubMed: 21665971 
• DOI: https://doi.org/10.1128/JB.00447-11
• Primary Citation of Related Structures:  
  3RYA, 3RYB


• PubMed Abstract: 
  

  Lactococcal oligopeptide-binding protein A (OppA) binds peptides with widely varied lengths and sequences. We previously hypothesized that a hydrophobic pocket in OppA preferentially binds a hydrophobic peptide side chain and thus determines its binding register. Two crystal structures of OppA with different nonapeptides now indeed show binding in different registers.

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Organizational Affiliation: 

Biochemistry Department, Groningen Biomolecular Sciences and Biotechnology Center, NPC & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 66.08 kDa 
• Atom Count: 5,361 
• Modelled Residue Count: 572 
• Deposited Residue Count: 599 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide-binding protein oppA	A	590	Lactococcus cremoris subsp. cremoris MG1363	Mutation(s): 0  Gene Names: llmg_0701, oppA
UniProt
Find proteins for A2RJ53 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore A2RJ53  Go to UniProtKB:  A2RJ53

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide	B	9	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.379	α = 100.66
b = 58.921	β = 101.31
c = 61.404	γ = 103.45

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-29 
Deposition Author(s): Berntsson, R.P.-A., Thunnissen, A.-M.W.H., Poolman, B., Slotboom, D.-J.

Revision History  

• Version 1.0: 2011-06-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description