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- PDB-8ovl: NMR solution structure of the heavy metal binding domain of P1B-A... -

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Basic information

Entry
Database: PDB / ID: 8ovl
TitleNMR solution structure of the heavy metal binding domain of P1B-ATPase LpCopA.
ComponentsCopper-translocating P-type ATPase
KeywordsMETAL BINDING PROTEIN / ATPase / metal binding / SilB-like fold
Function / homology
Function and homology information


ATPase-coupled monoatomic cation transmembrane transporter activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
Heavy metal binding domain / Heavy metal binding domain / P-type ATPase, subfamily IB / 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 ...Heavy metal binding domain / Heavy metal binding domain / P-type ATPase, subfamily IB / 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
Similarity search - Domain/homology
Copper-translocating P-type ATPase
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsNielsen, T.J.
Funding support Denmark, Sweden, 15items
OrganizationGrant numberCountry
LundbeckfondenR133-A12689 Denmark
LundbeckfondenR313-2019-774 Denmark
Danish National Research Foundation Denmark
Knut and Alice Wallenberg Foundation2015.0131 Sweden
Knut and Alice Wallenberg Foundation2020.0194 Sweden
The Carlsberg FoundationCF15-0542 Denmark
The Carlsberg FoundationCF21-0647 Denmark
Novo Nordisk FoundationNNF16OC0021272 Denmark
Other privateA29519 Denmark
Other private16-1992 Denmark
Other private20170818, 20180652 & 20200739 Sweden
Other private38267 Denmark
Danish Council for Independent Research9039-00273 Denmark
Swedish Research Council2016-04474 & 2022-01315 Sweden
Danish National Research FoundationDNRF 59 Denmark
CitationJournal: To Be Published
Title: NMR solution structure of the heavy metal binding domain of P1B-ATPase LpCopA.
Authors: Nielsen, J.T.
History
DepositionApr 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-translocating P-type ATPase


Theoretical massNumber of molelcules
Total (without water)9,1871
Polymers9,1871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 400target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Copper-translocating P-type ATPase


Mass: 9187.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues 1-35 and 71-83 are disordered and, hence, are not modeled in the coordinate file
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: copA1 / Production host: Yeast two-hybrid vector pC-ACT.1 (others) / References: UniProt: Q8RNP6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D 1H-15N TOCSY
161isotropic13D 1H-15N NOESY
171isotropic13D HN(CA)CB
181isotropic13D 1H-13C NOESY
1122isotropic12D 1H-15N HSQC
1112isotropic12D 1H-13C HSQC
1102isotropic13D 1H-15N NOESY
192isotropic13D 1H-13C NOESY
1132isotropic13D HNCO
1142isotropic13D H(CCO)NH
1152isotropic13D H(CCO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1100 mg/mL [U-100% 13C; U-100% 15N] Heavy metal binding domain (HMBD) of LpCopA, 50 mM 2-(N-morpholino)ethanesulfonic acid, 100 mM KCl, 2 mM TCEP (tris(2-carboxyethyl)phosphine), 90% H2O/10% D2OHMBD apo90% H2O/10% D2O
solution2100 mg/mL [U-100% 13C; U-100% 15N] Heavy metal binding domain (HMBD) of LpCopA, 13 mM AgNO3, 50 mM 2-(N-morpholino)ethanesulfonic acid, 100 mM KCl, 2 mM TCEP (tris(2-carboxyethyl)phosphine), 90% H2O/10% D2OHMBD Ag bound90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mg/mLHeavy metal binding domain (HMBD) of LpCopA[U-100% 13C; U-100% 15N]1
50 mM2-(N-morpholino)ethanesulfonic acidnatural abundance1
100 mMKClnatural abundance1
2 mMTCEP (tris(2-carboxyethyl)phosphine)natural abundance1
100 mg/mLHeavy metal binding domain (HMBD) of LpCopA[U-100% 13C; U-100% 15N]2
13 mMAgNO3natural abundance2
50 mM2-(N-morpholino)ethanesulfonic acidnatural abundance2
100 mMKClnatural abundance2
2 mMTCEP (tris(2-carboxyethyl)phosphine)natural abundance2
Sample conditionsIonic strength: 100 mM KCl mM / Label: Buffer / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2 / Details: Xplor-NIH
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 10

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