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- PDB-1nm4: Solution structure of Cu(I)-CopC from Pseudomonas syringae -

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Basic information

Entry
Database: PDB / ID: 1nm4
TitleSolution structure of Cu(I)-CopC from Pseudomonas syringae
ComponentsCopper resistance protein C
KeywordsMETAL BINDING PROTEIN / copper trafficking / redox switch / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


copper ion transport / response to copper ion / periplasmic space / copper ion binding / plasma membrane
Similarity search - Function
Copper transport protein C/D / : / CopC domain / CopC domain / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Copper resistance protein C / Copper resistance protein C
Similarity search - Component
Biological speciesPseudomonas syringae (bacteria)
MethodSOLUTION NMR / simulated annealing torsion angle dynamics restrained energy minimization
Model type detailsminimized average
AuthorsArnesano, F. / Banci, L. / Bertini, I. / Mangani, S. / Thompsett, A.R. / Structural Proteomics in Europe (SPINE)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: A redox switch in CopC: An intriguing copper trafficking protein that binds copper(I) and copper(II) at different sites
Authors: Arnesano, F. / Banci, L. / Bertini, I. / Mangani, S. / Thompsett, A.R.
History
DepositionJan 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper resistance protein C


Theoretical massNumber of molelcules
Total (without water)10,5471
Polymers10,5471
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein Copper resistance protein C / CopC


Mass: 10547.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Gene: COPC / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: P12376, UniProt: Q4ZWC7*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 13C-separated NOESY
1313D 15N-separated NOESY
141HNHA
151HNHB
NMR detailsText: Cu(I)-CopC was obtained by reducing Cu(II)-CopC with one equivalent of sodium ascorbate

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Sample preparation

DetailsContents: 2.5 mM Cu(I)-CopC 15N,13C; 100mM phosphate buffer NA; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM phosphate / pH: 7.0 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRprocessing
XEASYEccles, Guentert, Billeter, Wuethrichdata analysis
DYANAGuentert, Mumenthaler, Wuethrichstructure solution
CORMABorgias, Thomas, Jamesiterative matrix relaxation
Amber6Case, Kollman et al.refinement
RefinementMethod: simulated annealing torsion angle dynamics restrained energy minimization
Software ordinal: 1
Details: 1464 meaningful NOEs, 129 dihedral angle restraints and 34 experimental hydrogen bonds
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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