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- PDB-1nee: Structure of archaeal translation factor aIF2beta from Methanobac... -

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Basic information

Entry
Database: PDB / ID: 1nee
TitleStructure of archaeal translation factor aIF2beta from Methanobacterium thermoautrophicum
ComponentsProbable translation initiation factor 2 beta subunit
KeywordsTRANSLATION / two domain protein / mixed alpha-beta structure / Zinc finger
Function / homology
Function and homology information


translation initiation factor activity
Similarity search - Function
Alpha-Beta Plaits - #3150 / Translation initiation factor 2, beta subunit / 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor 2 subunit beta
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodSOLUTION NMR / The structures are based on 1142 NOE-derived constraints, 118 dihedral angle restraints, 39 hydrogen bonds, 58 NH residual dipolar couplings
AuthorsGutierrez, P. / Trempe, J.F. / Siddiqui, N. / Arrowsmith, C. / Gehring, K.
CitationJournal: Protein Sci. / Year: 2004
Title: Structure of the archaeal translation initiation factor aIF2beta from Methanobacterium thermoautotrophicum: Implications for translation initiation.
Authors: Gutierrez, P. / Osborne, M.J. / Siddiqui, N. / Trempe, J.F. / Arrowsmith, C. / Gehring, K.
History
DepositionDec 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)15,9592
Polymers15,8931
Non-polymers651
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 acceptable covalent geometry
RepresentativeModel #1

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Components

#1: Protein Probable translation initiation factor 2 beta subunit / eIF-2-beta


Mass: 15893.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: MTH1769 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O27797
#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
1113D 15N-separated NOESY
121HNHA
131HN(CA)CB
141CBCA(CO)NH
2513D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1~1.0mM aIF2beta, 50mM tris buffer, 300mM NaCl, 50uM ZnCl2, 1mM DTT, pH 6.0, 90% H2O, 10% D2O90% H2O/10% D2O
2~1.0mM aIF2beta, 50mM tris buffer, 300mM NaCl, 50uM ZnCl2, 1mM DTT, pH 6.0, 100% D2O100% D2O
Sample conditionspH: 6.0 / Pressure: 1 atm / Temperature: 310 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
Varian UNITYPLUSVarianUNITYPLUS8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukercollection
Gifa4.31Delsucprocessing
XEASY1.3.13Wutrichdata analysis
CNS0.9Brungerrefinement
ARIA1.1Nilgesstructure solution
RefinementMethod: The structures are based on 1142 NOE-derived constraints, 118 dihedral angle restraints, 39 hydrogen bonds, 58 NH residual dipolar couplings
Software ordinal: 1
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 100 / Conformers submitted total number: 20

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