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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2RJ53
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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