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- PDB-8bxj: apo structure of the specific silver chaperone needed for bacteri... -

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Basic information

Entry
Database: PDB / ID: 8bxj
Titleapo structure of the specific silver chaperone needed for bacterial silver resistance
ComponentsCopper ABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Silver binding protein periplasmic protein plasmid-encoded protein bacteria silver resistance metal coordination
Function / homologyCopper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / 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 8, 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


Theoretical massNumber of molelcules
Total (without water)10,7111
Polymers10,7111
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
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

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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
122isotropic12D 1H-13C HSQC aliphatic
142isotropic12D 1H-13C HSQC aromatic
151isotropic12D 1H-1H TOCSY
192isotropic12D (HB)CB(CGCD)HD
162isotropic13D CBCA(CO)NH
172isotropic13D HN(CA)CB
182isotropic13D HNCO
1102isotropic13D HNCA
1112isotropic13D HN(CO)CA
1122isotropic13D HBHA(CO)NH
1132isotropic13D (H)CCH-TOCSY
1142isotropic13D (H)CCH-TOCSY
1152isotropic13D 1H-15N TOCSY
1162isotropic13D 1H-13C NOESY
1172isotropic13D 1H-15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1300 uM SilF, 20 mM MES, 100 mM NaCl, 100% D2O1H100% D2O
solution2500 uM [U-100% 13C; U-100% 15N] SilF, 20 mM MES, 100 mM NaCl, 93% H2O/7% D2OU-13C,U-15N93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMSilFnatural abundance1
20 mMMESnatural abundance1
100 mMNaClnatural abundance1
500 uMSilF[U-100% 13C; U-100% 15N]2
20 mMMESnatural abundance2
100 mMNaClnatural abundance2
Sample conditionsIonic strength: 220 mM / Label: condition_1 / pH: 6.8 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Bruker 600 / Manufacturer: Bruker / Model: 600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.01Bruker 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 using WaterRefCNS from Pr. Roberto Tejero
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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