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- PDB-6eyg: Structure of a OpuBC mutant with bound Glycine betaine -

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Basic information

Entry
Database: PDB / ID: 6eyg
TitleStructure of a OpuBC mutant with bound Glycine betaine
ComponentsOsmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC
KeywordsTRANSPORT PROTEIN / substrate binding protein / ABC transporter / importer
Function / homology
Function and homology information


response to stress / amino acid transport / response to stimulus / 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
TRIMETHYL GLYCINE / Choline ABC transporter substrate-binding lipoprotein OpuBC / Choline-binding protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsPeherstorfer, S. / Teichmann, L. / Smits, S.H. / Schmitt, L. / Bremer, E.
CitationJournal: To Be Published
Title: Structure of a OpuBC mutant with bound Glycine betaine
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 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Osmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5492
Polymers34,4311
Non-polymers1181
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint5 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.750, 66.210, 63.590
Angle α, β, γ (deg.)90.00, 94.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Osmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC


Mass: 34430.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WE mutated this residue to alter the substrate specifictiy
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3194 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164TT67, UniProt: Q45462*PLUS
#2: Chemical ChemComp-BET / TRIMETHYL GLYCINE / Trimethylglycine


Mass: 118.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 1.81 Å3/Da / Density % sol: 32.21 %
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: 1.42→63.4 Å / Num. obs: 45559 / % possible obs: 98.2 % / Redundancy: 7.1 % / Rsym value: 0.13 / Net I/σ(I): 10.2
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 6.9 % / Num. unique obs: 4452 / Rsym value: 0.77 / % possible all: 97.3

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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: 1.42→63.4 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.429 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21933 2196 4.8 %RANDOM
Rwork0.18078 ---
obs0.1827 43364 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.12 Å2
2---0.09 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.42→63.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2221 0 8 301 2530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022280
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.9773077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.91925.45599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.48615424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.094156
X-RAY DIFFRACTIONr_chiral_restr0.1420.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211690
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: 1.42→1.457 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 137 -
Rwork0.295 3086 -
obs--97.2 %

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