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- PDB-2l55: Solution structure of the C-terminal domain of SilB from Cupriavi... -

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Basic information

Entry
Database: PDB / ID: 2l55
TitleSolution structure of the C-terminal domain of SilB from Cupriavidus metallidurans
ComponentsSilB,Silver efflux protein, MFP component of the three components proton antiporter metal efflux system
KeywordsMETAL BINDING PROTEIN / apo form / Ag(I)-binding site / Cu(I)-binding site / CusF ortholog
Function / homology
Function and homology information


transmembrane transporter activity / membrane / metal ion binding
Similarity search - Function
Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / Heavy metal binding domain / Heavy metal binding domain / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / OB fold (Dihydrolipoamide Acetyltransferase, E2P) ...Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF / Copper binding periplasmic protein CusF superfamily / Heavy metal binding domain / Heavy metal binding domain / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
SilB,Silver efflux protein, MFP component of the three components proton antiporter metal efflux system
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodSOLUTION NMR / simulated annealing, simulated annealing, molecular dynamics
Model detailsfewest violations, model 1
AuthorsBersch, B. / Derfoufi, K. / Vandenbussche, G.
CitationJournal: Biochemistry / Year: 2011
Title: Structural and Metal Binding Characterization of the C-Terminal Metallochaperone Domain of Membrane Fusion Protein SilB from Cupriavidus metallidurans CH34.
Authors: Bersch, B. / Derfoufi, K.M. / De Angelis, F. / Auquier, V. / Ngonlong Ekende, E. / Mergeay, M. / Ruysschaert, J.M. / Vandenbussche, G.
History
DepositionOct 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SilB,Silver efflux protein, MFP component of the three components proton antiporter metal efflux system


Theoretical massNumber of molelcules
Total (without water)8,5511
Polymers8,5511
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein SilB,Silver efflux protein, MFP component of the three components proton antiporter metal efflux system / Silver efflux protein


Mass: 8550.808 Da / Num. of mol.: 1 / Fragment: unp residues 440-521
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: Rmet_6135, silB / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AF3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1222D 1H-13C HSQC
1323D HNCO
1423D HN(CA)CB
1523D HN(CO)CA
1623D HN(COCA)CB
1723D-intraHNCA
1823D-intraHN(CA)CB
1922D 1H-15N HADAMAC
11023D C(CO)NH
11113D 1H-15N NOESY
11223D 1H-13C NOESY
11332D 1H-1H NOESY
1141T1 relaxation
1151T1rho relaxation
1161T2 relaxation
1171Heteronuclear NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 15N] protein, 50 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] protein, 50 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 15N] protein, 50 mM MES, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMSilB(440-521)-1[U-100% 15N]1
50 mMMES-21
1 mMSilB(440-521)-3[U-100% 13C; U-100% 15N]2
50 mMMES-42
1 mMSilB(440-521)-5[U-100% 15N]3
50 mMMES-63
Sample conditionsIonic strength: 50 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNMRSVarianVNMRS6002
Varian VNMRSVarianVNMRS6003

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VnmrJVariancollection
NMRViewJohnson, One Moon Scientificdata analysis
BATCHLescop, Brutscherchemical shift assignment
UNIO08Torsten Herrmannpeak picking
UNIO08Torsten Herrmannchemical shift assignment
UNIO08Torsten Herrmannstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
curvefitAG Palmerdata analysis
TALOSCornilescu, Delaglio and Baxdetermination of dihedral angles
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing, simulated annealing, molecular dynamics
Software ordinal: 1 / Details: CYANA (UNIO08), CNS, CNS, water refinement
NMR constraintsNOE constraints total: 1597
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: -6.5 ° / Maximum upper distance constraint violation: 0.39 Å
NMR ensemble rmsDistance rms dev: 0.022 Å / Distance rms dev error: 0.001 Å

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