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- PDB-6grv: Cadmium(II) form of full-length metallothionein from Pseudomonas ... -

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Basic information

Entry
Database: PDB / ID: 6grv
TitleCadmium(II) form of full-length metallothionein from Pseudomonas fluorescens Q2-87 (PflQ2 MT)
ComponentsMetallothionein
KeywordsMETAL BINDING PROTEIN / metallothionein / cadmium 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 12, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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)9,2725
Polymers8,8231
Non-polymers4504
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area7460 Å2
MethodPISA
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: 8822.591 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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
171isotropic12D 1H-15N HSQC
181isotropic12D 1H-13C HSQC aliphatic
191isotropic12D 1H-13C HSQC aromatic
111isotropic13D HNCO
121isotropic13D HN(CO)CA
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
1171isotropic13D HBHA(CO)NH
151isotropic13D (H)CCH-TOCSY
1121isotropic13D (H)CCH-TOCSY
1161isotropic12D (HB)CB(CGCD)HD
1151isotropic12D (HB)CB(CGCDCE)HE
161isotropic33D 1H-15N NOESY
1101isotropic33D 1H-13C NOESY aliphatic
1111isotropic13D 1H-13C NOESY aromatic
2142isotropic21D 113Cd
2132isotropic22D 1H-113Cd HSQC-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] metallothionein, 2 mM cadmium ion, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution21.5 mM metallothionein, 6 mM U-113CD cadmium ion, 50 mM [U-2H] TRIS, 50 mM sodium chloride, 90% H2O/10% D2O113Cd_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMmetallothionein[U-13C; U-15N]1
2 mMcadmium ionnatural abundance1
50 mMTRIS[U-2H]1
50 mMsodium chloridenatural abundance1
1.5 mMmetallothioneinnatural abundance2
6 mMcadmium ionU-113CD2
50 mMTRIS[U-2H]2
50 mMsodium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPH errPressure (kPa)Temperature (K)
150 mMconditions_17.4 0.21 atm300 K
250 mMconditions_27.4 0.21 atm320 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE6001CRYO TCI inverse triple-resonance (1H; 13C; 15N) probe with a cold 13C-Channel and an actively shielded z-gradient coil
Bruker AVANCEBrukerAVANCE7003CRYO TXI inverse triple-resonance (1H; 13C; 15N) with an actively shielded z-gradient coil
Bruker AVANCE IIBrukerAVANCE II5002CRYO 5 mm BBO probe with an actively shielded z-gradient coil

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4Bruker Biospincollection
TopSpin3.5Bruker Biospinprocessing
CARA1.9.1Keller and Wuthrichchemical shift assignment
UNIO2.02Hermannpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
Xplor-NIH4Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
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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