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- PDB-6eyh: Crystal structure of OpuBC in complex with DMSP -

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Basic information

Entry
Database: PDB / ID: 6eyh
TitleCrystal structure of OpuBC in complex with DMSP
ComponentsCholine binding protein OpuBC
KeywordsTRANSPORT PROTEIN / substrate binding protein / ABC transporter / importer
Function / homology
Function and homology information


cellular response to sulfate starvation / amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Osmoprotection protein (prox); domain 2 / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / Choline-binding protein
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis str. 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPeherstorfer, S. / Teichmann, L. / Smits, S.H. / Schmitt, L. / Bremer, E.
CitationJournal: To Be Published
Title: Structure of a OpuBC mutant with bound DMSP
Authors: Peherstorfer, S. / Teichmann, L. / Smits, S.H. / Schmitt, L. / Bremer, E.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Mar 4, 2026Group: Structure summary / Category: pdbx_entry_details / struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline binding protein OpuBC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5672
Polymers34,4311
Non-polymers1361
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.770, 65.890, 63.580
Angle α, β, γ (deg.)90.00, 92.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Choline binding protein OpuBC


Mass: 34430.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: Q45462
#2: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 1.81 Å3/Da / Density % sol: 32.04 %
Crystal growTemperature: 273 K / Method: batch mode / pH: 5
Details: 150 to 225 mM potassium acetate and 20% to 27.5% polyethylene glycol 3350
PH range: 4-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.6→63.5 Å / Num. obs: 32423 / % possible obs: 99.88 % / Redundancy: 4.9 % / Rsym value: 0.083 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3238 / Rsym value: 0.39 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R6U

3r6u


Resolution: 1.6→63.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.789 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20983 1563 4.8 %RANDOM
Rwork0.16927 ---
obs0.1713 30871 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.038 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20.14 Å2
2--0.44 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: 1 / Resolution: 1.6→63.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 8 279 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.022383
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9743227
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02625.243103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34815449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.417158
X-RAY DIFFRACTIONr_chiral_restr0.1510.2350
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211792
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 130 -
Rwork0.22 2244 -
obs--99.96 %

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