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- PDB-5a4g: NMR structure of a 180 residue construct encompassing the N-termi... -

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Basic information

Entry
Database: PDB / ID: 5a4g
TitleNMR structure of a 180 residue construct encompassing the N-terminal metal-binding site and the membrane proximal domain of SilB from Cupriavidus metallidurans CH34
ComponentsSILB, SILVER EFFLUX PROTEIN, MFP COMPONENT OF THE THREE COMPONENTS PROTON ANTIPORTER METAL EFFLUX SYSTEM
KeywordsMETAL BINDING PROTEIN / MEMBRANE FUSION PROTEIN / METAL SITE / SILVER / RESISTANCE NODULATION CELL DIVISION / RND
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 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
Similarity search - Domain/homology
SILVER ION / Silver efflux protein
Similarity search - Component
Biological speciesCUPRIAVIDUS METALLIDURANS (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsBersch, B. / Urbina Fernandez, P. / Vandenbussche, G.
CitationJournal: Biochemistry / Year: 2016
Title: Structural and Functional Investigation of the Ag+/Cu+-Binding Domains of the Periplasmic Adaptor Protein Silb from Cupriavidus Metallidurans Ch34.
Authors: Urbina, P. / Bersch, B. / De Angelis, F. / Derfoufi, K. / Prevost, M. / Goormaghtigh, E. / Vandenbussche, G.
History
DepositionJun 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1752
Polymers19,0681
Non-polymers1081
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000TOTAL ENERGY
RepresentativeModel #1

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Components

#1: Protein SILB, SILVER EFFLUX PROTEIN, MFP COMPONENT OF THE THREE COMPONENTS PROTON ANTIPORTER METAL EFFLUX SYSTEM / AG_SILBNM2


Mass: 19067.613 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 36-123,344-426
Source method: isolated from a genetically manipulated source
Details: THE CONSTRUCT IS NUMBERED 1-180,1 BEING THE N-TERMINAL METHIONINE. THE TWO PARTS OF THE MEMBRANE PROXIMAL DOMAIN ARE LINKED BY GS LOOP (RESIDUES 90 AND 91, CONSTRUCT NUMBERING)
Source: (gene. exp.) CUPRIAVIDUS METALLIDURANS (bacteria) / Strain: CH34 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58AF3
#2: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag
Sequence detailsCONSTRUCT RESIDUES 2-89 CORRESPOND TO Q58AF3 36-123, RESIDUES 92-174 CORRESPOND TO Q58AF3 344-426

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C EDITED NOESY
121CNOESY- ATNOS
23113C EDITED NOESY
241AROMNOESY-ATNOS (CENTERED ON AROMATIC CARBONS)
351EXPT 13
361NNOESY ATNOS
NMR detailsText: STRUCTURES CREATED BY ARIA2, WATER REFINEMENT.

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Sample preparation

DetailsContents: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
106.31.0 atm298.0 K
206.31.0 atm298.0 K
306.31.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8501
Bruker AVANCEBrukerAVANCE8502
Bruker AVANCEBrukerAVANCE9503

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Processing

NMR software
NameVersionDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNS1.1structure solution
NMRDrawANYstructure solution
NMRPipeANYstructure solution
CcpNmr Analysis2.3structure solution
CcpNmr Analysis2.4structure solution
NMRViewANYstructure solution
CYANAANYstructure solution
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: WATER REFINEMENT
NMR ensembleConformer selection criteria: TOTAL ENERGY / Conformers calculated total number: 1000 / Conformers submitted total number: 20

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