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- PDB-1jjd: NMR structure of the Cyanobacterial Metallothionein SmtA -

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Basic information

Entry
Database: PDB / ID: 1jjd
TitleNMR structure of the Cyanobacterial Metallothionein SmtA
ComponentsMETALLOTHIONEIN
KeywordsMETAL BINDING PROTEIN / zinc finger / zinc cluster / metallothionein
Function / homologyRibosomal Protein L24e; Chain: T; - #10 / Metallothionein, family 14, prokaryote / Prokaryotic metallothionein / Metallothionein domain superfamily / Ribosomal Protein L24e; Chain: T; / Roll / Mainly Beta / metal ion binding / Metallothionein
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / distance geometry, torsion angle dynamics
Model type detailsminimized average
AuthorsSadler, P.J. / Robinson, N.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: A metallothionein containing a zinc finger within a four-metal cluster protects a bacterium from zinc toxicity.
Authors: Blindauer, C.A. / Harrison, M.D. / Parkinson, J.A. / Robinson, A.K. / Cavet, J.S. / Robinson, N.J. / Sadler, P.J.
History
DepositionJul 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)5,8795
Polymers5,6171
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 500DIANA target function
RepresentativeModel #1minimized average structure

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Components

#1: Protein METALLOTHIONEIN / / SmtA


Mass: 5617.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Gene: smtA / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30331
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
222HNHA
3332D [1H,111Cd] HSQC
NMR detailsText: the average structure was calculated from the best 20 conformers.

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Sample preparation

Details
Solution-IDContentsSolvent system
13mM Zn4SmtA; 50 mM [D-11]TRIS/HCl buffer; 50mM NaCl;90% H2O/10% D2O
20.4mM 15N labelled Zn-SmtA; 50 mM [D-11]TRIS/HCl buffer; 50mM NaCl;90% H2O/10% D2O
33mM Cd4SmtA; 50 mM [D-11]TRIS/HCl buffer; 50mM NaCl;90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM NaCl 7.0 ambient 308 K
250mM NaCl 7.0 ambient 308 K
350mM NaCl 7.0 ambient 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYVarianUNITY6001
Bruker DMXBrukerDMX5002
Bruker DMXBrukerDMX3603

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1cVariancollection
XwinNMR2.1Brukerprocessing
SYBYL6.3Tripos inc.data analysis
DIANA2.2.1Wuethrich et alstructure solution
SYBYL6.3Tripos, Inc.refinement
RefinementMethod: distance geometry, torsion angle dynamics / Software ordinal: 1
Details: the structure is based on a total of 380 restraints, 291 are NOE-derived distance restraints, 37 are dihedral angle restraints, and 52 are zinc-ligand distance restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: DIANA target function / Conformers calculated total number: 500 / Conformers submitted total number: 1

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