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- PDB-1j5l: NMR STRUCTURE OF THE ISOLATED BETA_C DOMAIN OF LOBSTER METALLOTHI... -

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Basic information

Entry
Database: PDB / ID: 1j5l
TitleNMR STRUCTURE OF THE ISOLATED BETA_C DOMAIN OF LOBSTER METALLOTHIONEIN-1
ComponentsMETALLOTHIONEIN-1
KeywordsMETAL BINDING PROTEIN / beta-domain / Metalloprotein / Cadmium-sulfur-cluster
Function / homologyMetallothionein, crustacean / Metallothionein domain superfamily / metal ion binding / : / Metallothionein-1
Function and homology information
MethodSOLUTION NMR / ab initio simulated annealing
AuthorsMunoz, A. / Forsterling, F.H. / Shaw III, C.F. / Petering, D.H.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2002
Title: Structure of the (113)Cd(3)beta domains from Homarus americanus metallothionein-1: hydrogen bonding and solvent accessibility of sulfur atoms
Authors: Munoz, A. / Forsterling, F.H. / Shaw III, C.F. / Petering, D.H.
History
DepositionMay 16, 2002Deposition site: RCSB / Processing site: RCSB
SupersessionMay 22, 2002ID: 1HZQ
Revision 1.0May 22, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 5, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / database_2 ...atom_site / database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 2.2May 8, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METALLOTHIONEIN-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4714
Polymers3,1341
Non-polymers3373
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide METALLOTHIONEIN-1 / CUMT-1


Mass: 3133.726 Da / Num. of mol.: 1 / Fragment: BETA_C DOMAIN (RESIDUES 29-58) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homarus americanus (American lobster).
References: UniProt: P29499
#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
111DQF-COSY
1212D NOESY
1312D TOCSY
1412D 113Cd HSQC-TOCSY
1522D NOESY
162DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
12-3mM 113Cd3-MT-beta_C, 5mM d-Tris buffer90% H2O/10% D2O
22-3mM 113Cd3-MT-beta_C, 5mM d-Tris buffer100% D2O
Sample conditionsIonic strength: 5mM Tris / pH: 7.4 / Pressure: ambient / Temperature: 298 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 DRXBrukerDRX5001
Bruker DPXBrukerDPX3002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Bruker Instrumentscollection
XwinNMR2.5Bruker Instrumentsprocessing
Felix2000MSIdata analysis
X-PLOR3.851Axel Brungerstructure solution
MOLMOL2k.1Reto Koradidata analysis
X-PLOR3.851Axel Brungerrefinement
RefinementMethod: ab initio simulated annealing / Software ordinal: 1
Details: The structure is based on 228 NOE based distance restraints, 20 dihedral angle restraints and 33 metal cluster restraints derived from 113Cd-HSQC-TOCSY experiments.
NMR ensembleConformers submitted total number: 1

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