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- PDB-5nxy: Crystal structure of OpuAC from B. subtilis in complex with Arsen... -

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Basic information

Entry
Database: PDB / ID: 5nxy
TitleCrystal structure of OpuAC from B. subtilis in complex with Arsenobetaine
ComponentsOsmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC
KeywordsCHOLINE-BINDING PROTEIN / substrate binding protein Arseen / B. subtilis
Function / homology
Function and homology information


response to stress / 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
2-(trimethyl-lambda~5~-arsanyl)ethanol / Choline ABC transporter substrate-binding lipoprotein OpuBC / Choline-binding protein
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHofmann, T. / Bremer, E. / Schmitt, L. / Smits, S.
CitationJournal: Environ. Microbiol. / Year: 2018
Title: Arsenobetaine: an ecophysiologically important organoarsenical confers cytoprotection against osmotic stress and growth temperature extremes.
Authors: Hoffmann, T. / Warmbold, B. / Smits, S.H.J. / Tschapek, B. / Ronzheimer, S. / Bashir, A. / Chen, C. / Rolbetzki, A. / Pittelkow, M. / Jebbar, M. / Seubert, A. / Schmitt, L. / Bremer, E.
History
DepositionMay 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,5535
Polymers64,1612
Non-polymers3923
Water6,143341
1
A: Osmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3083
Polymers32,0801
Non-polymers2272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Osmotically activated L-carnitine/choline ABC transporter substrate-binding protein OpuCC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2462
Polymers32,0801
Non-polymers1651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.200, 117.400, 68.700
Angle α, β, γ (deg.)90.00, 104.00, 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: 32080.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N terminus was deleted on expression plasmid / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3194 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A164TT67, UniProt: Q45462*PLUS
#2: Chemical ChemComp-1Y8 / 2-(trimethyl-lambda~5~-arsanyl)ethanol


Mass: 165.086 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H14AsO
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 3350, 0.2M potassium acetate, pH 8.7, VAPOR DIFFUSION, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 31660 / % possible obs: 95.1 % / Redundancy: 2 % / Net I/σ(I): 17.2

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R6U

3r6u


Resolution: 1.9→19.835 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2508 2256 5 %
Rwork0.1934 --
obs0.1963 45110 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 18 341 4672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084497
X-RAY DIFFRACTIONf_angle_d1.1146071
X-RAY DIFFRACTIONf_dihedral_angle_d14.1081712
X-RAY DIFFRACTIONf_chiral_restr0.079655
X-RAY DIFFRACTIONf_plane_restr0.005775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.3011360.22472576X-RAY DIFFRACTION96
1.9413-1.98640.29771400.20442672X-RAY DIFFRACTION98
1.9864-2.03610.28611400.21092652X-RAY DIFFRACTION98
2.0361-2.09110.29431410.21122690X-RAY DIFFRACTION98
2.0911-2.15250.27221420.21032682X-RAY DIFFRACTION98
2.1525-2.22190.32211410.20882683X-RAY DIFFRACTION98
2.2219-2.30120.29061380.20852624X-RAY DIFFRACTION97
2.3012-2.39320.25991420.19992699X-RAY DIFFRACTION98
2.3932-2.50190.261410.19862671X-RAY DIFFRACTION98
2.5019-2.63350.26781400.2032679X-RAY DIFFRACTION98
2.6335-2.79810.27621430.21212699X-RAY DIFFRACTION98
2.7981-3.01350.26161410.21792682X-RAY DIFFRACTION98
3.0135-3.31550.28711420.21642702X-RAY DIFFRACTION98
3.3155-3.79230.23491430.19322713X-RAY DIFFRACTION98
3.7923-4.76690.19751420.14652711X-RAY DIFFRACTION98
4.7669-19.83610.17141440.15842719X-RAY DIFFRACTION98

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