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- PDB-1nd9: Solution Structure of the N-terminal Subdomain of Translation Ini... -

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Basic information

Entry
Database: PDB / ID: 1nd9
TitleSolution Structure of the N-terminal Subdomain of Translation Initiation Factor IF2
ComponentsTranslation initiation factor IF-2
KeywordsTRANSLATION / IF2 / initiation factor
Function / homology
Function and homology information


guanosine tetraphosphate binding / ribosomal small subunit binding / : / translation initiation factor activity / response to cold / translational initiation / GTPase activity / GTP binding / membrane / cytoplasm / cytosol
Similarity search - Function
Putative DNA-binding domain, N-terminal subdomain of bacterial translation initiation factor IF2 / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 ...Putative DNA-binding domain, N-terminal subdomain of bacterial translation initiation factor IF2 / Initiation factor 2 associated domain, bacterial / Bacterial translation initiation factor IF-2 associated region / Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / Phenylalanyl-tRNA Synthetase; Chain B, domain 1 / Translation initiation factor IF-2, domain II / Initiation factor 2 signature. / Translation initiation factor IF-2, bacterial-like / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / : / Elongation factor G domain 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Putative DNA-binding domain superfamily / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor IF-2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsLaursen, B.S. / Mortensen, K.K. / Sperling-Petersen, H.U. / Hoffman, D.W.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: A conserved structural motif at the N terminus of bacterial translation initiation factor IF2
Authors: Laursen, B.S. / Mortensen, K.K. / Sperling-Petersen, H.U. / Hoffman, D.W.
History
DepositionDec 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: Translation initiation factor IF-2


Theoretical massNumber of molelcules
Total (without water)5,4061
Polymers5,4061
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 20structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Representative

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Components

#1: Protein/peptide Translation initiation factor IF-2


Mass: 5405.960 Da / Num. of mol.: 1 / Fragment: N-terminal Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: K12 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0A705

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2212D NOESY
1322D NOESY
1433D 15N-separated NOESY
1543D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM IF2 (res 2-157); 10 mM Phosphate buffer90% H2O/10% D2O
22mM IF2 (res 2-157); 10 mM Phosphate buffer100% D2O
32mM IF2 (res 2-157); 15N; 10 mM Phosphate buffer90% H2O/10% D2O
42mM IF2 (res 2-157); 15N;13C; 10 mM Phosphate buffer90% H2O/10% D2O
52mM IF2 (res 2-157); K-15N; 10 mM Phosphate buffer90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM Phosphate 6ambient 298 K
210 mM Phosphate 6ambient 308 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 software
NameVersionDeveloperClassification
Felix1Hare Research Inc.processing
NMRPipe1Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J. and Bax, Aprocessing
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L.structure solution
CNS1.1Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 996 restraints, 918 are NOE-derived distance constraints, 63 dihedral angle restraints,15 distance restraints from hydrogen bonds.
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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