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- PDB-2mfp: Solution structure of the circular g-domain analog from the wheat... -

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Basic information

Entry
Database: PDB / ID: 2mfp
TitleSolution structure of the circular g-domain analog from the wheat metallothionein Ec-1
ComponentsEC protein I/II
KeywordsMETAL BINDING PROTEIN / Metallothionein / Metal-thiolate cluster / Backbone cyclized protein
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 / molecular dynamics, simulated annealing
AuthorsTarasava, K. / Johannsen, S. / Freisinger, E.
CitationJournal: Molecules / Year: 2013
Title: Solution Structure of the Circular gamma-Domain Analog from the Wheat Metallothionein Ec-1.
Authors: Tarasava, K. / Johannsen, S. / Freisinger, E.
History
DepositionOct 14, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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.pdbx_leaving_atom_flag / _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_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 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _pdbx_entry_details.has_protein_modification

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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)3,0173
Polymers2,7921
Non-polymers2252
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 2792.142 Da / Num. of mol.: 1 / Fragment: GAMMA DOMAIN (UNP residues 2-27)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Plasmid: pTWIN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P30569
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THESE RESIDUES ARE ARTIFICIAL ONES THAT WERE INSERTED AS LINKER TO ENABLE THE ...AUTHORS STATE THAT THESE RESIDUES ARE ARTIFICIAL ONES THAT WERE INSERTED AS LINKER TO ENABLE THE CYCLIZATION OF THIS SMALL GAMMA-DOMAIN.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
1312D 1H-113Cd HSQC
2412D 1H-1H TOCSY
2512D 1H-1H NOESY
2612D 1H-113Cd HSQC

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Sample preparation

DetailsContents: 0.9 mM cyc-gEc1, 1.8 mM 113Cd CADMIUM ION, 10 mM [U-99% 2H] TRIS, 10 mM sodium perchlorate, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMcyc-gEc1-11
1.8 mMCADMIUM ION-2113Cd1
10 mMTRIS-3[U-99% 2H]1
10 mMsodium perchlorate-41
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.027.5ambient 307.2 K
20.027.5ambient 295.5 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE6002
Bruker DRXBrukerDRX5003

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.9.0Keller and Wuthrichchemical shift assignment
CARA1.9.0Keller and Wuthrichpeak picking
CARA1.9.0Keller and Wuthrichdata analysis
CYANA3.1Guntert, Mumenthaler and Wuthrichstructure solution
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddarddata analysis
XEASY1.3.13Bartels et al.data analysis
XEASY1.3.13Bartels et al.peak picking
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.33Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpin3Bruker Biospinprocessing
TopSpin3Bruker Biospincollection
PSVSBhattacharya and Montelionevalidation
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: RESTRAINT REFINEMENT IN EXPLICIT SOLVENT (WATER), IN TORSION COORDINATES USING NOEASSIGN ALGORITHM
NMR constraintsNOE constraints total: 201 / NOE long range total count: 21 / NOE medium range total count: 38
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20
NMR ensemble rmsDistance rms dev: 0.8 Å

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