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- PDB-8c2q: Silver ion-bound structure of the silver specific chaperone SilF ... -

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Basic information

Entry
Database: PDB / ID: 8c2q
TitleSilver ion-bound structure of the silver specific chaperone SilF needed for bacterial silver resistance
ComponentsCopper ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Silver bound protein periplasmic protein plasmid-encoded protein bacteria silver resistance metal coordination METAL BINDING PROTEIN
Function / homologyCopper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / SILVER ION / Copper ABC transporter substrate-binding protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsMonneau, Y.R. / Walker, O. / Hologne, M.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The battle for silver binding: How the interplay between the SilE, SilF, and SilB proteins contributes to the silver efflux pump mechanism.
Authors: Arrault, C. / Monneau, Y.R. / Martin, M. / Cantrelle, F.X. / Boll, E. / Chirot, F. / Comby Zerbino, C. / Walker, O. / Hologne, M.
History
DepositionDec 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8192
Polymers10,7111
Non-polymers1081
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints, chemical shift perturbations upon Ag(I) binding
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area120 Å2
ΔGint-6 kcal/mol
Surface area7240 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein Copper ABC transporter substrate-binding protein


Mass: 10711.252 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: ORF96 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZHD1
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
162isotropic12D 1H-13C HSQC aliphatic
122isotropic12D 1H-13C HSQC aromatic
132isotropic13D CBCA(CO)NH
142isotropic13D HN(CA)CB
152isotropic13D HNCA
172isotropic13D HN(CO)CA
182isotropic13D HNCO
192isotropic13D HBHA(CO)NH
1102isotropic13D (H)CCH-TOCSY
1112isotropic13D (H)CCH-TOCSY
1122isotropic13D 1H-15N TOCSY
1132isotropic13D 1H-15N NOESY
1142isotropic13D 1H-13C NOESY
1151isotropic12D TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM SilF, 20 mM MES, 100 mM NaCl, 330 uM Ag(I), 100% D2Onatural abundance100% D2O
solution2500 uM [U-100% 13C; U-100% 15N] SilF, 20 mM MES, 100 mM NaCl, 550 uM Ag(I), 95% H2O/5% D2Odouble-labeled95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMSilFnatural abundance1
20 mMMESnatural abundance1
100 mMNaClnatural abundance1
330 uMAg(I)natural abundance1
500 uMSilF[U-100% 13C; U-100% 15N]2
20 mMMESnatural abundance2
100 mMNaClnatural abundance2
550 uMAg(I)natural abundance2
Sample conditionsIonic strength: 220 mM / Label: Cond_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRFAM-SPARKYBioinformatics. 2015 Apr 15; 31(8):1325-7. Epub 2014 Dec 12 NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Lee W, Tonelli M, Markley JLchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: water refinement
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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