3FTO

Crystal structure of OppA in a open conformation

• PDB DOI: https://doi.org/10.2210/pdb3FTO/pdb

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


• Deposited: 2009-01-13 Released: 2009-03-31 
• Deposition Author(s): Berntsson, R.P.-A., Oktaviani, N.A., Fusetti, F., Thunnissen, A.-M.W.H., Poolman, B., Slotboom, D.-J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.276 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Literature

Selenomethionine incorporation in proteins expressed in Lactococcus lactis.

Berntsson, R.P., Alia Oktaviani, N., Fusetti, F., Thunnissen, A.M., Poolman, B., Slotboom, D.J.

(2009) Protein Sci 18: 1121-1127

• PubMed: 19388077 
• DOI: https://doi.org/10.1002/pro.97
• Primary Citation of Related Structures:  
  3FTO


• PubMed Abstract: 
  

  Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a protocol for incorporation of selenomethionine (SeMet) into proteins expressed in L. lactis. Incorporation efficiencies of SeMet in the membrane protein complex OpuA (an ABC transporter) and the soluble protein OppA, both from L. lactis, were monitored by mass spectrometry. Both proteins incorporated SeMet with high efficiencies (>90%), which greatly extends the usefulness of the expression host L. lactis for X-ray crystallography purposes. The crystal structure of ligand-free OppA was determined at 2.4 A resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.

---

Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 65.8 kDa 
• Atom Count: 4,589 
• Modelled Residue Count: 559 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligopeptide-binding protein oppA	A	590	Lactococcus cremoris	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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.276 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.577	α = 90
b = 122.287	β = 102.05
c = 59.408	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-31 
Deposition Author(s): Berntsson, R.P.-A., Oktaviani, N.A., Fusetti, F., Thunnissen, A.-M.W.H., Poolman, B., Slotboom, D.-J.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary