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- PDB-5mn3: NMR structure of the Littorina littorea metallothionein, a snail ... -

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Basic information

Entry
Database: PDB / ID: 5mn3
TitleNMR structure of the Littorina littorea metallothionein, a snail MT folding into three distinct domains
Componentsdomain-swapped metallothionein from Littorina Littorea
KeywordsMETAL TRANSPORT / NMR metallothionein metal cluster
Function / homology:
Function and homology information
Biological speciesLittorina litorea (invertebrata)
MethodSOLUTION NMR / molecular dynamics
AuthorsZerbe, O. / Jurt, S. / Baumann, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationI 1482-N28 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2017
Title: Structural Adaptation of a Protein to Increased Metal Stress: NMR Structure of a Marine Snail Metallothionein with an Additional Domain.
Authors: Baumann, C. / Beil, A. / Jurt, S. / Niederwanger, M. / Palacios, O. / Capdevila, M. / Atrian, S. / Dallinger, R. / Zerbe, O.
History
DepositionDec 12, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.2Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jul 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: domain-swapped metallothionein from Littorina Littorea
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,20710
Polymers10,1961
Non-polymers1,0129
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein domain-swapped metallothionein from Littorina Littorea


Mass: 10195.717 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: residues wt(8-38) are exchanged with ds(40-70) and wt(41-70) with ds(8-37)
Source: (gene. exp.) Littorina litorea (invertebrata) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) / Variant (production host): pLysS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: Cd
Details: residues wt(8-38) are exchanged with ds(40-70) and wt(41-70) with ds(8-37)
Source: (gene. exp.) Littorina litorea (invertebrata) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3) / Variant (production host): pLysS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
191isotropic22D 1H-15N HSQC
151isotropic22D 1H-13C HSQC aliphatic
111isotropic13D HNCO
121isotropic13D HN(CA)CO
131isotropic13D HN(COCA)CB
141isotropic13D HN(CA)CB
171isotropic13D (H)CCH-TOCSY
161isotropic13D 13C-NOESY
1102isotropic13D 15N-NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 13C; U-99% 15N] ds-LlMT, 90% H2O/10% D2O15N,13C Sample90% H2O/10% D2O
solution20.5 mM [U-99% 15N] ds-LlMT, 90% H2O/10% D2O15N sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMds-LlMT[U-99% 13C; U-99% 15N]1
0.5 mMds-LlMT[U-99% 15N]2
Sample conditionsDetails: 0.5mM ds-LlMT 20 mM TRIS 1mM TSP / Ionic strength: 20 mM / Ionic strength err: 2 / Label: sample_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 bar / Pressure err: 0.1 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CARA2.8Keller and Wuthrichchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
CNS-XPLORBrunger, Schwietersrefinement
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20

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