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- PDB-1m0j: solution structure of the beta domain of mt_nc -

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Basic information

Entry
Database: PDB / ID: 1m0j
Titlesolution structure of the beta domain of mt_nc
Componentsmetallothionein MT_nc
KeywordsMETAL BINDING PROTEIN / cadmium thiolate-cluster
Function / homology
Function and homology information


detoxification of copper ion / intracellular zinc ion homeostasis / cellular response to zinc ion / cellular response to copper ion / cellular response to cadmium ion / positive regulation of ERK1 and ERK2 cascade / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Metallothionein, vertebrate / Metallothionein, vertebrate, metal binding site / Metallothionein domain superfamily, vertebrate / Metallothionein / Vertebrate metallothioneins signature. / Metallothionein domain superfamily
Similarity search - Domain/homology
: / Metallothionein A
Similarity search - Component
Biological speciesNotothenia coriiceps (black rockcod)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCapasso, C. / Carginale, V. / Crescenzi, O. / Di Maro, D. / Parisi, E. / Spadaccini, R. / Temussi, P.A.
CitationJournal: Structure / Year: 2003
Title: Solution Structure of MT_nc, a Novel Metallothionein from the Antarctic Fish Notothenia coriiceps.
Authors: Capasso, C. / Carginale, V. / Crescenzi, O. / Di Maro, D. / Parisi, E. / Spadaccini, R. / Temussi, P.A.
History
DepositionJun 13, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: metallothionein MT_nc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,1504
Polymers2,8131
Non-polymers3373
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide metallothionein MT_nc / metallothionein A


Mass: 2813.218 Da / Num. of mol.: 1 / Fragment: beta domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Notothenia coriiceps (black rockcod) / Plasmid details: pCR2.1-TOPO / Plasmid: PGEM-MT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62339
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / 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-IDType
1112D NOESY
1212D TOCSY
131E-COSY
141DQF-COSY
152[113Cd,1H]COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM metallothionein; 95% H2O, 5% D2O95% H2O/5% D2O
2metallothionein, U-113Cd; 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionspH: 7 / Pressure: ambient / Temperature: 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX4001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
NMRView4.0.3Johnsonndata analysis
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 253 NOEs, 12 Cd-S bonds and 63 dihedral angle constraints
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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