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- PDB-2kak: Solution structure of the beta-E-domain of wheat Ec-1 metallothionein -

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Basic information

Entry
Database: PDB / ID: 2kak
TitleSolution structure of the beta-E-domain of wheat Ec-1 metallothionein
ComponentsEC protein I/II
KeywordsMETAL BINDING PROTEIN / metallothionein / solution structure / wheat Ec-1 / Zn binding / Metal-binding / Metal-thiolate cluster / Zinc
Function / homologyPlant EC metallothionein-like protein, family 15 / Plant PEC family metallothionein / zinc ion binding / EC protein I/II
Function and homology information
Biological speciesTriticum aestivum (bread wheat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPeroza, E.A. / Schmucki, R. / Guntert, P. / Freisinger, E. / Zerbe, O.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The beta(E)-domain of wheat E(c)-1 metallothionein: a metal-binding domain with a distinctive structure.
Authors: Peroza, E.A. / Schmucki, R. / Guntert, P. / Freisinger, E. / Zerbe, O.
History
DepositionNov 6, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_spectrometer ...pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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: EC protein I/II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3465
Polymers5,0851
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein EC protein I/II / Zinc metallothionein class II


Mass: 5084.617 Da / Num. of mol.: 1 / Fragment: UNP residues 31-81
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Production host: Escherichia coli (E. coli) / Strain (production host): K12 / Variant (production host): BL21(DE3) / References: UniProt: P30569
#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 1H-1H NOESY
1212D 1H-1H TOCSY
1323D 1H-15N TOCSY
1423D 1H-15N NOESY
NMR detailsText: CYS-METAL CONNECITIVITES HAVE BEEN ASSIGNED TENTATIVELY USING COMPUTATIONAL METHODS

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM EC protein, 15.0 mM TRIS, 50.0 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-99% 15N] EC protein, 15.0 mM TRIS, 50.0 mM NaCl, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMentity_11
15.0 mMTRIS1
50.0 mMNaCl1
1.0 mMentity_1[U-99% 15N]2
15.0 mMTRIS2
50.0 mMNaCl2
Sample conditionsIonic strength: 50 / pH: 6.8 / Pressure: AMBIENT / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3P. Guntert et al.refinement
CYANA3P. Guntert et al.structure solution
OPALpR. Koradi, P. Guntert, M. Billeterrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 539 / NOE intraresidue total count: 129 / NOE long range total count: 168 / NOE medium range total count: 111 / NOE sequential total count: 192
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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