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- PDB-1sb6: Solution structure of a cyanobacterial copper metallochaperone, ScAtx1 -

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Basic information

Entry
Database: PDB / ID: 1sb6
TitleSolution structure of a cyanobacterial copper metallochaperone, ScAtx1
Componentscopper chaperone ScAtx1
KeywordsCHAPERONE / copper chaperone / new metal binding motif / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


Heavy-metal-associated, conserved site / Heavy-metal-associated domain. / Heavy-metal-associated domain / Heavy metal-associated domain superfamily / Heavy-metal-associated domain profile. / Heavy metal-associated domain, HMA / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Su, X.C. / Borrelly, G.P. / Robinson, N.J. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Solution Structures of a Cyanobacterial Metallochaperone: INSIGHT INTO AN ATYPICAL COPPER-BINDING MOTIF.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Su, X.C. / Borrelly, G.P. / Robinson, N.J.
History
DepositionFeb 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

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Assembly

Deposited unit
A: copper chaperone ScAtx1


Theoretical massNumber of molelcules
Total (without water)6,6911
Polymers6,6911
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 / 200the submitted structures are the 20 structures with the lowest target function of 200 conformers
Representative

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Components

#1: Protein copper chaperone ScAtx1


Mass: 6690.513 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Plasmid: pETATX1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P73213

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
1312D TOCSY
141HNHA
NMR detailsText: The structure was determined using 15N labelled apo ScAtx1

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Sample preparation

DetailsContents: 0.7 mM apoScAtx1,50mM phosphate, 90%H2O, 10%D2O / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM phosphate / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3Xia, Bartlesstructure solution
DYANA1.5Gunter, Mumenthaler, Wuthrichstructure solution
Amber5Pealman, Case, Caldwell, Ross, Cheatham, Ferguson,Seibel, Singh, Weiner, Kollmanrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: In the ensemble each structure is based on a total of 1017 meaningful NOEs constrants together with 44 dihedral angle(phi)restraints.
NMR ensembleConformer selection criteria: the submitted structures are the 20 structures with the lowest target function of 200 conformers
Conformers calculated total number: 200 / Conformers submitted total number: 20

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