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- PDB-1oq3: A core mutation affecting the folding properties of a soluble dom... -

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Basic information

Entry
Database: PDB / ID: 1oq3
TitleA core mutation affecting the folding properties of a soluble domain of the ATPase protein CopA from Bacillus subtilis
ComponentsPotential copper-transporting ATPase
KeywordsHYDROLASE / CopA / NMR / folding / P-type ATPase / mutation / 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-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_ref_seq_dif
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_ref_seq_dif.details
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: Potential copper-transporting ATPase


Theoretical massNumber of molelcules
Total (without water)8,1741
Polymers8,1741
Non-polymers00
Water0
1


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

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Components

#1: Protein Potential copper-transporting ATPase


Mass: 8174.431 Da / Num. of mol.: 1 / Fragment: N-terminal water soluble domain 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): pLysS / References: UniProt: O32220, Cu2+-exporting ATPase

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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: 3132 NOE cross peaks were assigned and integrated, providing 1960 unique upper distance limits, of which 1440 are meaningful. A total of 41 proton pairs were stereospecifically assigned.

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Sample preparation

DetailsContents: 1.5 mM apoD1S46V, 20mM phosphate, 90%H2O, 10%D2O,2.0mDTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20mM phosphate + 2mM DTT / pH: 7.0 / Pressure: 1 atm / 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 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
NMR ensembleConformer selection criteria: The submitted conformer models are the 30 structures with the lowest violations
Conformers calculated total number: 300 / Conformers submitted total number: 30

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