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- PDB-2ofg: Solution structure of the n-terminal domain of the zinc(II) ATPas... -

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Basic information

Entry
Database: PDB / ID: 2ofg
TitleSolution structure of the n-terminal domain of the zinc(II) ATPase ziaa in its apo form
ComponentsZinc-transporting ATPase
KeywordsHYDROLASE / MEMBRANE PROTEIN / FERREDOXIN-LIKE FOLD / BETA-ALPHA-BETA-BETA-ALPHA-BETA / STRUCTURAL GENOMICS
Function / homology
Function and homology information


P-type Zn2+ transporter / P-type zinc transporter activity / cadmium ion transmembrane transporter activity / zinc ion transport / metal ion transport / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / 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
Zinc-transporting ATPase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodSOLUTION NMR / Simulated Annealing in TAD, Restrained Energy Minimization
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Poggi, L. / Robinson, N.J. / Vanarotti, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2010
Title: NMR structural analysis of the soluble domain of ZiaA-ATPase and the basis of selective interactions with copper metallochaperone Atx1.
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Poggi, L. / Vanarotti, M. / Tottey, S. / Waldron, K.J. / Robinson, N.J.
History
DepositionJan 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: 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
X: Zinc-transporting ATPase


Theoretical massNumber of molelcules
Total (without water)12,0711
Polymers12,0711
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)30 / 300target function
Representative

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Components

#1: Protein Zinc-transporting ATPase / E.C.3.6.3.5 / Zn(2+)-translocating P-type ATPase


Mass: 12070.612 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ZIAA / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q59998, EC: 3.6.3.5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
1323D 15N-separated NOESY
1433D 13C-separated NOESY
152HNHA
163HNCA-J

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM unlabeledH2O/D2O 90:10
21.0 mM 15N-labeledH2O/D2O 90:10
31.0mM 15N,13C labeledH2O/D2O 90:10
Sample conditionsIonic strength: 50mM phosphate buffer / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE7003
Bruker AVANCEBrukerAVANCE8004
Bruker AVANCEBrukerAVANCE9005

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guentert, P., Mumenthaler, C. Wuethrich, Kstructure solution
Amber8PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSONrefinement
RefinementMethod: Simulated Annealing in TAD, Restrained Energy Minimization
Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

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