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- PDB-3l6g: Crystal structure of lactococcal OpuAC in its open conformation -

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Basic information

Entry
Database: PDB / ID: 3l6g
TitleCrystal structure of lactococcal OpuAC in its open conformation
ComponentsBetaine ABC transporter permease and substrate binding protein
KeywordsGLYCINE BETAINE-BINDING PROTEIN / glycine betaine binding / substrate binding domain / venus fly-trap / Cell membrane / Membrane / Transmembrane / Transport
Function / homology
Function and homology information


amine transmembrane transporter activity / carnitine transmembrane transporter activity / glycine betaine transport / choline transport / peptide transport / ATP-binding cassette (ABC) transporter complex / protein transport
Similarity search - Function
Glycine betaine-binding periplasmic protein; domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile. / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Betaine ABC transporter permease and substrate binding protein
Similarity search - Component
Biological speciesLactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsBerntsson, R.P.A. / Wolters, J.C. / Gul, N. / Karasawa, A. / Thunnissen, A.M.W.H. / Slotboom, D.J. / Poolman, B.
CitationJournal: Plos One / Year: 2010
Title: Ligand binding and crystal structures of the substrate-binding domain of the ABC transporter OpuA.
Authors: Wolters, J.C. / Berntsson, R.P. / Gul, N. / Karasawa, A. / Thunnissen, A.M. / Slotboom, D.J. / Poolman, B.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Betaine ABC transporter permease and substrate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8302
Polymers28,5471
Non-polymers2821
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.131, 68.131, 109.143
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Betaine ABC transporter permease and substrate binding protein


Mass: 28547.410 Da / Num. of mol.: 1 / Fragment: substrate binding domain (UNP residues 320-573)
Source method: isolated from a genetically manipulated source
Details: The substrate binding domain at the C-terminal of the ABC-transporter OpuA
Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria)
Strain: NZ9000 / Gene: busAB, LL1451, L724, L72477 / Plasmid: pNZ9000 / Production host: Lactococcus lactis (lactic acid bacteria) / Strain (production host): NZ9000 / References: UniProt: Q7DAU8
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane pH 8.5, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 1.9→44.5 Å / Num. obs: 20918 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 24.533 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 15.62
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-2.010.5423.919408327898.9
2.01-2.150.3286.4188213113100
2.15-2.320.238.9175452917100
2.32-2.550.1611.9162752709100
2.55-2.850.10916147752467100
2.85-3.280.07222.2129382185100
3.28-4.020.04631.710864188699.7
4.02-5.660.03837.38214147999.5
5.660.03437.2451788498.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å48.18 Å
Translation2.5 Å48.18 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.2.0phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4L

2b4l


Resolution: 1.9→44.073 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.89 / SU ML: 0.21 / σ(F): 2 / σ(I): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 1046 5 %
Rwork0.167 --
obs0.169 20914 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.989 Å2 / ksol: 0.422 e/Å3
Displacement parametersBiso max: 79.44 Å2 / Biso mean: 21.301 Å2 / Biso min: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.045 Å20 Å20 Å2
2---0.045 Å2-0 Å2
3---0.089 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 19 280 2304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172095
X-RAY DIFFRACTIONf_angle_d1.4282842
X-RAY DIFFRACTIONf_chiral_restr0.103309
X-RAY DIFFRACTIONf_plane_restr0.007358
X-RAY DIFFRACTIONf_dihedral_angle_d18.805781
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.899-1.9990.2631440.1912743288799
1.999-2.1240.2111460.15827772923100
2.124-2.2880.191480.14928132961100
2.288-2.5180.1981480.15128172965100
2.518-2.8830.2181490.16228322981100
2.883-3.6320.1891520.1628813033100
3.632-44.0850.1891590.183005316499

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