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- PDB-1k81: NMR Structure of the Zinc-Ribbon Domain within Translation Initia... -

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Basic information

Entry
Database: PDB / ID: 1k81
TitleNMR Structure of the Zinc-Ribbon Domain within Translation Initiation Factor 2 Subunit beta
ComponentsPROBABLE TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT
KeywordsTRANSLATION / translation initiation factor / zinc ribbon
Function / homology
Function and homology information


formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / translation initiation factor activity
Similarity search - Function
Translation initiation factor 2, beta subunit / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5
Similarity search - Domain/homology
Translation initiation factor 2 subunit beta
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / simulated annealing
AuthorsCho, S. / Hoffman, D.W.
CitationJournal: Biochemistry / Year: 2002
Title: Structure of the beta Subunit of Translation Initiation Factor 2 from the Archaeon Methanococcus jannaschii: A Representative of the eIF2beta/eIF5 Family of Proteins
Authors: Cho, S. / Hoffman, D.W.
History
DepositionOct 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROBABLE TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1282
Polymers4,0621
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 170structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide PROBABLE TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT / EIF-2-BETA


Mass: 4062.103 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57562
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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
1213D 13C-separated NOESY
1313D 15N-separated ROESY
NMR detailsText: This structure was determined using standard 2D and 3D heteronuclear NMR techniques.

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Sample preparation

DetailsContents: 1 mM aIF2 beta U-15N,13C; 10 mM phosphate buffer / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.0 / Pressure: ambient / Temperature: 293 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 spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: CNS / Version: 1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 170 / Conformers submitted total number: 10

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