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- PDB-6gw8: Zn(II) form of shortened metallothionein from Pseudomonas fluores... -

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Basic information

Entry
Database: PDB / ID: 6gw8
TitleZn(II) form of shortened metallothionein from Pseudomonas fluorescens Q2-87 (residues 1-52)
Componentsmetallothionein
KeywordsMETAL BINDING PROTEIN / metallothionein / zinc(II) ion
Function / homologyMetallothionein, family 14, prokaryote / Prokaryotic metallothionein / Metallothionein domain superfamily / cadmium ion binding / zinc ion binding / Metallothionein
Function and homology information
Biological speciesPseudomonas fluorescens Q2-87 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsHabjanic, J. / Zerbe, O. / Freisinger, E.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Other governmentFK-15-085 Switzerland
Other governmentFK-17-091 Switzerland
CitationJournal: Metallomics / Year: 2018
Title: A histidine-rich Pseudomonas metallothionein with a disordered tail displays higher binding capacity for cadmium than zinc.
Authors: Habjanic, J. / Zerbe, O. / Freisinger, E.
History
DepositionJun 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...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: metallothionein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9644
Polymers5,7671
Non-polymers1963
Water0
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 metallothionein /


Mass: 5767.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens Q2-87 (bacteria)
Gene: PflQ2_2045 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: J2EKT7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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 aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCO
151isotropic13D HN(CA)CB
161isotropic13D HN(CO)CA
171isotropic13D CBCA(CO)NH
181isotropic13D HBHA(CO)NH
191isotropic13D (H)CCH-TOCSY
1101isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N NOESY
1121isotropic23D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic

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Sample preparation

DetailsType: solution
Contents: 0.5 mM [U-13C; U-15N] metallothionein, 1.5 mM ZINC ION, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMmetallothionein[U-13C; U-15N]1
1.5 mMZINC IONnatural abundance1
50 mMTRIS[U-2H]1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7.4 / PH err: 0.2 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001CRYO TCI inverse triple-resonance (1H; 13C; 15N) with a cold 13C-Channel and an actively shielded z-gradient coil
Bruker AVANCEBrukerAVANCE7002CRYO TXI inverse triple-resonance (1H; 13C; 15N) with an actively shielded z-gradient coil

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
CARA1.9.1.5Keller and Wuthrichchemical shift assignment
UNIO2.0.2Herrmannpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIH4Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 6
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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