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- PDB-1p6t: Structure characterization of the water soluble region of P-type ... -

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Basic information

Entry
Database: PDB / ID: 1p6t
TitleStructure characterization of the water soluble region of P-type ATPase CopA from Bacillus subtilis
ComponentsPotential copper-transporting ATPase
KeywordsHYDROLASE / CopA / P-type ATPase / water-soluble region / beta-alpha-beta-beta-alpha-beta fold / NMR / 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.Biol.Chem. / Year: 2003
Title: Structural basis for the function of the N-terminal domain of the ATPase CopA from Bacillus subtilis.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Gonnelli, L. / Su, X.C.
History
DepositionApr 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 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)16,4011
Polymers16,4011
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.
RepresentativeModel #1fewest violations

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Components

#1: Protein Potential copper-transporting ATPase


Mass: 16400.746 Da / Num. of mol.: 1 / Fragment: N-terminal water soluble region (residues 1-147) / 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 13C-separated NOESY
1413D 15N-separated NOESY
151HNHA
161HNHB
171CC(CO)NH
181(H)CCH-TOCSY
191CBCANH
1101CBCA(CO)NH
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.5 mM apoS46VCopA, 20mM phosphate, 90%H2O, 10%D2O,2.0 mMDTT
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 20 mM phosphate + 2 mM 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
Bruker AVANCEBrukerAVANCE5003
Bruker AVANCEBrukerAVANCE7004

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERprocessing
DYANA1.5Gunter, Mumenthaler, Wuthrichstructure solution
XEASY1.3Xia, Bartelsstructure 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: 5099 NOE cross peaks were assigned and integrated, providing 4102 unique upper distance limits, of which 3303 are meaningful. 152 angle constraints, were experimentally determined and used in the calculations.
NMR representativeSelection criteria: fewest violations
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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