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- PDB-1oq6: solution structure of Copper-S46V CopA from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1oq6
Titlesolution structure of Copper-S46V CopA from Bacillus subtilis
ComponentsPotential copper-transporting ATPase
KeywordsHYDROLASE / P-type ATPase / mutation / folding / Copper complex / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / 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 / E1-E2 ATPase ...Heavy metal-associated domain, copper ion-binding / P-type ATPase, subfamily IB / 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 / E1-E2 ATPase / P-type ATPase, haloacid dehalogenase domain / P-type ATPase, phosphorylation site / P-type ATPase, cytoplasmic domain N / E1-E2 ATPases phosphorylation site. / P-type ATPase, A domain superfamily / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-exporting P-type ATPase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics,
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gonnelli, l. / Su, X.C. / Structural Proteomics in Europe (SPINE)
CitationJournal: J.Mol.Biol. / Year: 2003
Title: A core mutation affecting the folding properties of a soluble domain of the ATPase protein CopA from Bacillus subtilis
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gonnelli, l. / Su, X.C.
History
DepositionMar 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Potential copper-transporting ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2382
Polymers8,1741
Non-polymers641
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 300structures with lowest energy violations
Representative

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Components

#1: Protein Potential copper-transporting ATPase


Mass: 8174.431 Da / Num. of mol.: 1 / Fragment: copper form of N-terminal S46V of CopA / Mutation: S46V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: YVGX / Plasmid: PET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O32220, Cu2+-exporting ATPase
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1313D 15N-separated NOESY
141HNHA
151HNHB
NMR detailsText: The structure was determined with 15N labeled sample.

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Sample preparation

DetailsContents: 1.2 mM Cu-D1S46VCopA, 20mM phosphate, 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 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
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukerprocessing
XEASY1.3Xia, Bartelsstructure solution
DYANA1.5Gunter, Mumenthaler, Wuthrichstructure solution
Amber5Pearlman, Case, Caldwell, Ross, cheatham, Ferguson, Seibel, Singh, Weiner, Kollmanrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics,
Software ordinal: 1
Details: 2913 NOE cross peaks were assigned and integrated, providing 1818 unique upper distance limits, of which 1357 are meaningful. A total of 35 proton pairs were stereospecifically assigned.
NMR ensembleConformer selection criteria: structures with lowest energy violations
Conformers calculated total number: 300 / Conformers submitted total number: 30

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