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- PDB-6qk6: Solution Structure of the Cd-loaded form of a Metallothionein fro... -

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Basic information

Entry
Database: PDB / ID: 6qk6
TitleSolution Structure of the Cd-loaded form of a Metallothionein from Helix Pomatia
ComponentsCadmium-metallothionein
KeywordsMETAL BINDING PROTEIN / metallothionein / Cadmium protein / snail protein / Helix pomatia
Function / homologyEukaryotic metallothionein / Metallothionein, mollusc / metal ion binding / : / Cadmium-metallothionein
Function and homology information
Biological speciesHelix pomatia (Roman snail)
MethodSOLUTION NMR / molecular dynamics
AuthorsZerbe, O. / Jurt, S. / Beil, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationDach Project grant No I 1482-N28 Switzerland
CitationJournal: Biochemistry / Year: 2019
Title: The Solution Structure and Dynamics of Cd-Metallothionein fromHelix pomatiaReveal Optimization for Binding Cd over Zn.
Authors: Beil, A. / Jurt, S. / Walser, R. / Schonhut, T. / Guntert, P. / Palacios, O. / Atrian, S. / Capdevila, M. / Dallinger, R. / Zerbe, O.
History
DepositionJan 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
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
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.4Jun 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: Cadmium-metallothionein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,3107
Polymers6,6361
Non-polymers6746
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cadmium-metallothionein / CD-MT


Mass: 6635.640 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: the first residue Gly is an artefact from cloning / Source: (gene. exp.) Helix pomatia (Roman snail) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Plys / References: UniProt: P33187
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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
121isotropic22D 1H-15N HSQC
132isotropic22D 1H-15N HSQC
142isotropic22D 1H-13C HSQC aliphatic
152isotropic13D CBCA(CO)NH
162isotropic13D HNCO
172isotropic13D HN(CA)CB
182isotropic13D (H)CCH-TOCSY
192isotropic23D 1H-13C NOESY aliphatic
1102isotropic23D 1H-15N NOESY
1112isotropic13D HBHA(CO)NH
1122isotropic13D HN(CA)CO

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution110 mM [U-2H] TRIS, 1 mM TSP, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution210 mM [U-2H] TRIS, 1 mM TSP, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMTRIS[U-2H]1
1 mMTSPnone1
10 mMTRIS[U-2H]2
1 mMTSPnone2
Sample conditionsIonic strength: 20 mM / Label: conditions_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1.0 atm / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker NeoBrukerNeo6001
Bruker NeoBrukerNeo7002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
CYANA3.85Guntert, Mumenthaler and Wuthrichstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CARAKeller and Wuthrichchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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