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- PDB-1d1n: SOLUTION STRUCTURE OF THE FMET-TRNAFMET BINDING DOMAIN OF BECILLU... -

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Basic information

Entry
Database: PDB / ID: 1d1n
TitleSOLUTION STRUCTURE OF THE FMET-TRNAFMET BINDING DOMAIN OF BECILLUS STEAROTHERMOPHILLUS TRANSLATION INITIATION FACTOR IF2
ComponentsINITIATION FACTOR 2
KeywordsGENE REGULATION / BETA-BARREL
Function / homology
Function and homology information


translation initiation factor activity / GTPase activity / GTP binding / cytosol
Similarity search - Function
Translation initiation factor IF-2, N-terminal / Translation initiation factor IF-2, N-terminal region / 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, N-terminal / Translation initiation factor IF-2, N-terminal region / 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 / Translation factors / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Translation initiation factor IF-2
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodSOLUTION NMR
AuthorsMeunier, S. / Spurio, S. / Czisch, M. / Wechselberger, R. / Gueunneugues, M.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the fMet-tRNA(fMet)-binding domain of B. stearothermophilus initiation factor IF2.
Authors: Meunier, S. / Spurio, R. / Czisch, M. / Wechselberger, R. / Guenneugues, M. / Gualerzi, C.O. / Boelens, R.
History
DepositionSep 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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: INITIATION FACTOR 2


Theoretical massNumber of molelcules
Total (without water)11,2111
Polymers11,2111
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)20 / 50STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON- BOND ENERGY,STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1closest to the average

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Components

#1: Protein INITIATION FACTOR 2


Mass: 11210.744 Da / Num. of mol.: 1 / Fragment: C2 TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: P04766

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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Processing

NMR representativeSelection criteria: closest to the average
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: 50 / Conformers submitted total number: 20

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