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

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Basic information

Entry
Database: PDB / ID: 5nxx
TitleCrystal structure of OpuAC from B. subtilis in complex with Arsenobetaine
ComponentsGlycine betaine ABC transport system glycine betaine-binding protein OpuAC
KeywordsTRANSPORT PROTEIN / substrate binding protein Arseen / B. subtilis
Function / homology
Function and homology information


amino acid transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / membrane raft
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 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(trimethylarsonio)acetate / Betaine-binding protein OpuAC / Glycine betaine-binding protein OpuAC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 28, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Glycine betaine ABC transport system glycine betaine-binding protein OpuAC
D: Glycine betaine ABC transport system glycine betaine-binding protein OpuAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9184
Polymers59,5622
Non-polymers3562
Water6,233346
1
C: Glycine betaine ABC transport system glycine betaine-binding protein OpuAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9592
Polymers29,7811
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Glycine betaine ABC transport system glycine betaine-binding protein OpuAC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9592
Polymers29,7811
Non-polymers1781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.100, 30.000, 106.100
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycine betaine ABC transport system glycine betaine-binding protein OpuAC / Glycine betaine/proline transport system substrate-binding protein


Mass: 29780.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N terminus not visible in x-ray structure / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_1321, SAMN05878487_3340 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A085C2M9, UniProt: P46922*PLUS
#2: Chemical ChemComp-3Q7 / (trimethylarsonio)acetate


Mass: 178.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11AsO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, ammonium acetate, PEG 4000, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 274K

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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 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 27772 / % possible obs: 95.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 11.7
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.344

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B4M

2b4m


Resolution: 2.2→19.944 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 28.72
RfactorNum. reflection% reflection
Rfree0.282 1389 5 %
Rwork0.1835 --
obs0.1885 27772 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.944 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4132 0 16 346 4494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154314
X-RAY DIFFRACTIONf_angle_d1.4595843
X-RAY DIFFRACTIONf_dihedral_angle_d15.0841609
X-RAY DIFFRACTIONf_chiral_restr0.082642
X-RAY DIFFRACTIONf_plane_restr0.007735
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2005-2.2790.33451330.23262527X-RAY DIFFRACTION93
2.279-2.37010.32981390.21942639X-RAY DIFFRACTION98
2.3701-2.47780.33871410.20552688X-RAY DIFFRACTION98
2.4778-2.60820.29461380.19832625X-RAY DIFFRACTION98
2.6082-2.77120.30051410.20212661X-RAY DIFFRACTION97
2.7712-2.98450.29291400.19372667X-RAY DIFFRACTION97
2.9845-3.28360.28731380.18622621X-RAY DIFFRACTION97
3.2836-3.7560.25461390.16192640X-RAY DIFFRACTION96
3.756-4.72180.24471380.152616X-RAY DIFFRACTION95
4.7218-19.94470.2651420.17832699X-RAY DIFFRACTION93

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