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- PDB-1mwy: Solution structure of the N-terminal domain of ZntA in the apo-form -

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Basic information

Entry
Database: PDB / ID: 1mwy
TitleSolution structure of the N-terminal domain of ZntA in the apo-form
ComponentsZntA
KeywordsHYDROLASE / open-faced beta-sandwich fold / beta-alpha-beta-beta-alpha-beta
Function / homology
Function and homology information


detoxification of zinc ion / Cd2+-exporting ATPase / P-type Zn2+ transporter / P-type zinc transporter activity / lead ion transmembrane transporter activity / lead ion transport / cadmium ion transmembrane transport / P-type cadmium transporter activity / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / cadmium ion transmembrane transporter activity ...detoxification of zinc ion / Cd2+-exporting ATPase / P-type Zn2+ transporter / P-type zinc transporter activity / lead ion transmembrane transporter activity / lead ion transport / cadmium ion transmembrane transport / P-type cadmium transporter activity / Translocases; Catalysing the translocation of inorganic cations; Linked to the hydrolysis of a nucleoside triphosphate / cadmium ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / metal ion transport / intracellular zinc ion homeostasis / response to zinc ion / response to cadmium ion / response to lead ion / 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/cadmium/lead-transporting P-type ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsBanci, L. / Bertini, I. / Ciofi-Baffoni, S. / Finney, L.A. / Outten, C.E. / O'Halloran, T.V.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: A new zinc-protein coordination site in intracellular metal trafficking: solution structure of the apo and Zn(II) forms of ZntA (46-118)
Authors: Banci, L. / Bertini, I. / Ciofi-Baffoni, S. / Finney, L.A. / Outten, C.E. / O'Halloran, T.V.
History
DepositionOct 1, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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
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: ZntA


Theoretical massNumber of molelcules
Total (without water)7,9401
Polymers7,9401
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
RepresentativeModel #1lowest energy

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Components

#1: Protein ZntA / Lead / cadmium / zinc and mercury transporting ATPase


Mass: 7939.863 Da / Num. of mol.: 1 / Fragment: N-terminal domain, (residues 46-118)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: znta / Plasmid: pET11c / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P37617, EC: 3.6.3.3, 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
1113D 15N-separated NOESY
121HNHA
1322D NOESY
1422D TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.5 mM U-15N apo-ZntA(46-118), 100 mM phosphate buffer90% H2O/10% D2O
22.0 mM unlabelled apo-ZntA(46-118), 100 mM phosphate buffer90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM sodium phosphate / pH: 7 / Pressure: ambient / 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 AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Bruker softwarecollection
DYANA1.5Guentert P., Wuthrich K. et al.structure solution
CORMABorgias B., Thomas P.D., James T.L.iterative matrix relaxation
Amber5Case D.A., Pearlman D.A. et al.refinement
XEASY3.2Bartels C., Billiter M., Guentert P., Wuthrich K.data analysis
XwinNMR1.3Bruker softwareprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on 1772 NOE-derived distance constraints and 87 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 30

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