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- PDB-1j5m: SOLUTION STRUCTURE OF THE SYNTHETIC 113CD_3 BETA_N DOMAIN OF LOBS... -

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Basic information

Entry
Database: PDB / ID: 1j5m
TitleSOLUTION STRUCTURE OF THE SYNTHETIC 113CD_3 BETA_N DOMAIN OF LOBSTER METALLOTHIONEIN-1
ComponentsMETALLOTHIONEIN-1
KeywordsMETAL BINDING PROTEIN / Metallothionein / beta-domain / metal-sulfur-cluster / 2D-NMR / 113Cd-NMR / conformational changes / HN-S-hydrogen bonds
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: 1HZR
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 2.1Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.status_code_nmr_data / _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: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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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)3,1854
Polymers2,8471
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: 2847.406 Da / Num. of mol.: 1 / Fragment: BETA_N DOMAIN (RESIDUES 1-28) / 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
1112D-TOCSY
1212D-NOESY
131DQF-COSY
141PE-COSY
1512D-113Cd-HSQC-TOCSY
2612D-TOCSY
NMR detailsText: HN-S hydrogen bonds were determined using a 2D long range 1H{113Cd} HMQC experiment

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Sample preparation

DetailsContents: 5mM (113Cd)3-beta_N, 5mM d-Tris-HCl / Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
15mM Tris-HCl 7.4ambient 278 K
25mM Tris-HCl 7.4ambient 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
XwinNMR2.5Brukercollection
XwinNMR2.5Brukerprocessing
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 276 distance restraints, 240 derived from NOE, 33 metal cluster restraints from 113Cd HSQC TOCSY and 6 restraints from HN-S hydrogen bonds. A total of 27 dihedral ...Details: The structure is based on 276 distance restraints, 240 derived from NOE, 33 metal cluster restraints from 113Cd HSQC TOCSY and 6 restraints from HN-S hydrogen bonds. A total of 27 dihedral angle restraints was applied, 13 phi, 10 chi1 and 4 Cys-Cd chi2 angles. Methylene protons for which no stereospecific assignment could be obtained were treated with the floating chirality procedure in XPLOR.
NMR ensembleConformers submitted total number: 1

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