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- PDB-3l6h: Crystal structure of lactococcal OpuAC in its closed-liganded con... -

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Basic information

Entry
Database: PDB / ID: 3l6h
TitleCrystal structure of lactococcal OpuAC in its closed-liganded conformation complexed with glycine betaine
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


peptide transport / response to stimulus / transmembrane transporter activity / 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
TRIMETHYL GLYCINE / 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: 2.3 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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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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)28,7364
Polymers28,5471
Non-polymers1893
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.706, 111.706, 151.728
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-58-

HOH

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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-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M NaCl, 0.1 M Na-Hepes, pH 7.0, 20% PEG 6000, 1 mM glycine betaine, 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: Mar 11, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 2.2→46 Å / Num. obs: 16390 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.71
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obs% possible all
2.2-2.330.6662.596.1
2.33-2.490.4733.699
2.49-2.690.3225.398.4
2.69-2.950.2047.997.8
2.95-3.290.12811.597.5
3.29-3.80.07817.696.9
3.8-4.650.05523.596.6
4.65-6.540.04924.896.6
6.540.04128.795.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.35 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.78 Å
Translation2.5 Å40.78 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 3L6G

3l6g


Resolution: 2.3→40.78 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.237 / SU ML: 0.127 / SU R Cruickshank DPI: 0.257 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22137 819 5 %RANDOM
Rwork0.1972 ---
obs0.19843 15560 100 %-
all-16379 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.832 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0.53 Å2-0 Å2
2---1.05 Å20 Å2
3---1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 10 140 2145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222056
X-RAY DIFFRACTIONr_bond_other_d0.0010.021356
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.9382788
X-RAY DIFFRACTIONr_angle_other_deg0.77833355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9075255
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.81926.66787
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85815372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.882151
X-RAY DIFFRACTIONr_chiral_restr0.0520.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022260
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.221.51274
X-RAY DIFFRACTIONr_mcbond_other0.0321.5519
X-RAY DIFFRACTIONr_mcangle_it0.43822051
X-RAY DIFFRACTIONr_scbond_it0.73782
X-RAY DIFFRACTIONr_scangle_it1.1654.5737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 59 -
Rwork0.217 1137 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 16.9555 Å / Origin y: -6.4325 Å / Origin z: 47.3776 Å
111213212223313233
T0.0136 Å20.0198 Å20.0065 Å2-0.0503 Å20.0015 Å2--0.0822 Å2
L1.1253 °20.1362 °20.0608 °2-1.1435 °20.4615 °2--1.8801 °2
S0.0052 Å °0.1523 Å °0.0042 Å °0.0061 Å °0.0201 Å °-0.0325 Å °0.0448 Å °0.0148 Å °-0.0252 Å °

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