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- PDB-1dfs: SOLUTION STRUCTURE OF THE ALPHA-DOMAIN OF MOUSE METALLOTHIONEIN-1 -

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Basic information

Entry
Database: PDB / ID: 1dfs
TitleSOLUTION STRUCTURE OF THE ALPHA-DOMAIN OF MOUSE METALLOTHIONEIN-1
ComponentsMETALLOTHIONEIN-1
KeywordsMETAL BINDING PROTEIN / 3-10 HELIX / CD-S CLUSTER / HALF TURN
Function / homology
Function and homology information


cellular response to chromate / intracellular monoatomic cation homeostasis / negative regulation of growth / detoxification of copper ion / intracellular zinc ion homeostasis / cellular response to zinc ion / nitric oxide mediated signal transduction / cellular response to copper ion / cellular response to cadmium ion / negative regulation of neuron apoptotic process ...cellular response to chromate / intracellular monoatomic cation homeostasis / negative regulation of growth / detoxification of copper ion / intracellular zinc ion homeostasis / cellular response to zinc ion / nitric oxide mediated signal transduction / cellular response to copper ion / cellular response to cadmium ion / negative regulation of neuron apoptotic process / lysosome / copper ion binding / zinc ion binding / nucleus / metal ion binding / cytosol / 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-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
Model type detailsminimized average
AuthorsZangger, K. / Oz, G. / Otvos, J.D. / Armitage, I.M.
CitationJournal: Protein Sci. / Year: 1999
Title: Three-dimensional solution structure of mouse [Cd7]-metallothionein-1 by homonuclear and heteronuclear NMR spectroscopy.
Authors: Zangger, K. / Oz, G. / Otvos, J.D. / Armitage, I.M.
History
DepositionNov 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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_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 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METALLOTHIONEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4755
Polymers3,0261
Non-polymers4504
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 50MINIMIZED AVERAGE STRUCTURE
Representativeminimized average structure

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Components

#1: Protein/peptide METALLOTHIONEIN-1


Mass: 3025.702 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (ALPHA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02802
#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-IDType
1112D NOESY
1212D TOCSY
231ACCORDION CD-H HSQC
NMR detailsText: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR TECHNIQUES AND AN ACCORDION CD-H HSQC

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Sample preparation

DetailsContents: 0.7MM MOUSE-METALLOTHIONEIN-1, NATURAL ABUNDANCE, 15MM PHOSPHATE BUFFER NA
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
115mMKPI 6.5AMBIENT 283 K
215mMKPI 6.5AMBIENT 298 K
Crystal grow
*PLUS
Method: other

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITY INOVAVarianUNITY INOVA8001
Varian UNITY INOVAVarianUNITY INOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1AVARIANdata analysis
X-PLOR3.851BRUNGERstructure solution
X-PLOR3.851BRUNGERrefinement
RefinementMethod: HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
Software ordinal: 1
Details: A TOTAL OF 278 NOE-DERIVED DISTANCE CONSTRAINTS AND 16 CD-S CONNECTIVITIES
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE / Conformers calculated total number: 50 / Conformers submitted total number: 1

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