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- PDB-2ife: TRANSLATION INITIATION FACTOR IF3 FROM ESCHERICHIA COLI RIBOSOME ... -

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Basic information

Entry
Database: PDB / ID: 2ife
TitleTRANSLATION INITIATION FACTOR IF3 FROM ESCHERICHIA COLI RIBOSOME BINDING DOMAIN (RESIDUES 84-180)
ComponentsPROTEIN (TRANSLATION INITIATION FACTOR IF3)
KeywordsGENE REGULATION / INITIATION FACTOR
Function / homology
Function and homology information


ribosome disassembly / translation initiation factor activity / response to cold / ribosome binding / RNA binding / membrane / cytosol
Similarity search - Function
Translation initiation factor 3 (IF-3), C-terminal domain / Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain ...Translation initiation factor 3 (IF-3), C-terminal domain / Translation initiation factor 3, conserved site / Initiation factor 3 signature. / Translation initiation factor 3, C-terminal / Translation initiation factor IF-3, C-terminal domain / Translation initiation factor 3 / Translation initiation factor 3, N-terminal / Translation initiation factor 3 (IF-3), N-terminal domain superfamily / Translation initiation factor 3 (IF-3), C-terminal domain superfamily / Translation initiation factor IF-3, N-terminal domain / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Translation initiation factor IF-3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / DISTANCE GEOMETRY, RESTRAINED SIMULATED ANNEALING
AuthorsDe Cock, E. / Garcia, C. / Dardel, F.
Citation
Journal: To be Published
Title: Interaction of E. Coli Translation Initiation Factor If3 with the Ribosome
Authors: De Cock, E. / Blanquet, S. / Lallemand, J.-Y. / Dardel, F.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Solution Structure of the Ribosome-Binding Domain of E. Coli Translation Initiation Factor If3. Homology with the U1A Protein of the Eukaryotic Spliceosome
Authors: Garcia, C. / Fortier, P.-L. / Blanquet, S. / Lallemand, J.-Y. / Dardel, F.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: 1H and 15N Resonance Assignment and Structure of N-Terminal Domain of Escherichia Coli Initiation Factor 3
Authors: Garcia, C. / Fortier, P.-L. / Blanquet, S. / Lallemand, J.-Y. / Dardel, F.
#3: Journal: Biochimie / Year: 1994
Title: The N-Terminal of Initiation Factor If3 is Folded as a Stable Independent Domain
Authors: Fortier, P.-L. / Schmitter, J.-M. / Garcia, C. / Dardel, F.
History
DepositionDec 16, 1998Deposition site: BNL / Processing site: RCSB
SupersessionDec 23, 1998ID: 1IFE
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 1.4Dec 27, 2023Group: 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: PROTEIN (TRANSLATION INITIATION FACTOR IF3)


Theoretical massNumber of molelcules
Total (without water)11,7971
Polymers11,7971
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 200LOWEST TARGET FUNCTION
RepresentativeModel #2

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Components

#1: Protein PROTEIN (TRANSLATION INITIATION FACTOR IF3)


Mass: 11796.936 Da / Num. of mol.: 1 / Fragment: RIBOSOME-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: PRODUCT OF THE INFC GENE / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM83 / Gene: INFC CODONS 84-180 / Plasmid: PTRCINFCC / Gene (production host): INFC CODONS 84-180 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P0A707

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HMQC-NOESY
121(H)CCH-TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELLED SAMPLE

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Sample preparation

Sample conditionsIonic strength: 20 mM POTASSIUM PHOSPHATE / pH: 6.5 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker DRX600 / Manufacturer: Bruker / Model: DRX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DIANAstructure solution
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, RESTRAINED SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION
NMR ensembleConformer selection criteria: LOWEST TARGET FUNCTION / Conformers calculated total number: 200 / Conformers submitted total number: 24

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