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- PDB-2gcf: Solution structure of the N-terminal domain of the coppper(I) ATP... -

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Basic information

Entry
Database: PDB / ID: 2gcf
TitleSolution structure of the N-terminal domain of the coppper(I) ATPase PacS in its apo form
ComponentsCation-transporting ATPase pacS
KeywordsHYDROLASE / ferredoxin-like fold / beta-alpha-beta-beta-alpha-beta / Structural Genomics / Structural Proteomics in Europe / SPINE
Function / homology
Function and homology information


P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / copper ion homeostasis / intracellular copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding ...P-type divalent copper transporter activity / P-type monovalent copper transporter activity / P-type Cu+ transporter / copper ion export / copper ion import / copper ion homeostasis / intracellular copper ion homeostasis / copper ion binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
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, 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
Probable copper-transporting ATPase PacS
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Kandias, N.G. / Spyroulias, G.A. / Robinson, N.J. / Structural Proteomics in Europe (SPINE)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The delivery of copper for thylakoid import observed by NMR.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Kandias, N.G. / Robinson, N.J. / Spyroulias, G.A. / Su, X.C. / Tottey, S. / Vanarotti, M.
History
DepositionMar 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cation-transporting ATPase pacS


Theoretical massNumber of molelcules
Total (without water)7,9101
Polymers7,9101
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)21 / 200Minimized average structure
RepresentativeModel #1lower target funcion

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Components

#1: Protein Cation-transporting ATPase pacS


Mass: 7910.031 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 1-95
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: pacS / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P73241, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111CBCANH
121CBCA(CO)NH
1322D NOESY
1423D 15N-separated NOESY
152HNHA
1613D 13C-separated NOESY
171HNCA
181HN(CO)CA
191HNCO
1101(H)CCH-TOCSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM PacS U-15N,13C, 100mM Sodium phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
21.5mM PacS U-15N, 100mM Sodium phosphate buffer, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM sodium phosphate buffer / pH: 7 / Pressure: ambient / 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 AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE8004

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Processing

NMR software
NameVersionClassification
XwinNMR3.6collection
PSEUDYANA1.5structure solution
Amber8refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lower target funcion
NMR ensembleConformer selection criteria: Minimized average structure / Conformers calculated total number: 200 / Conformers submitted total number: 21

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