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- PDB-6vrj: Solution structure of Pseudomonas aeruginosa IF3 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 6vrj
TitleSolution structure of Pseudomonas aeruginosa IF3 C-terminal domain
ComponentsTranslation initiation factor IF-3
KeywordsTRANSLATION / translation initiation factor 3
Function / homology
Function and homology information


ribosome disassembly / translation initiation factor activity / ribosome binding / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Translation initiation factor IF-3 / Translation initiation factor IF-3
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, Y. / Li, L.
CitationJournal: To Be Published
Title: Solution structure of Pseudomonas aeruginosa IF3 C-terminal domain
Authors: Zhang, Y. / Li, L.
History
DepositionFeb 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Translation initiation factor IF-3


Theoretical massNumber of molelcules
Total (without water)11,2871
Polymers11,2871
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, molecular weight as monomer
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translation initiation factor IF-3


Mass: 11287.258 Da / Num. of mol.: 1 / Fragment: C-terminal domain residues 81-177
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: infC, IPC47_09970 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5E9LPE5, UniProt: Q9I0A0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-15N TOCSY
142isotropic23D CBCA(CO)NH
152isotropic23D HN(CA)CB
162isotropic23D HBHA(CO)NH
172isotropic23D C(CO)NH
182isotropic23D HNCO
193isotropic23D 1H-13C NOESY
1103isotropic23D (H)CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11.0 mM [U-15N] PaIF3C, 25 mM KPO4, 90% H2O/10% D2O25mM KPO4 buffer, DTT15N_sample90% H2O/10% D2O
solution21.0 mM [U-13C; U-15N] PaIF3C, 25 mM KPO4, 90% H2O/10% D2O25mM KPO4 buffer, DTT13C15N_sample90% H2O/10% D2O
solution31.0 mM [U-99% 13C; U-99% 15N] PaIF3C, 25 mM KPO4, 100% D2O25mM KPO4 buffer, DTT13C15ND2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMPaIF3C[U-15N]1
1.0 mMPaIF3C[U-13C; U-15N]2
1.0 mMPaIF3C[U-99% 13C; U-99% 15N]3
25 mMKPO4natural abundance1
25 mMKPO4natural abundance2
25 mMKPO4natural abundance3
Sample conditionsDetails: 25mM KPO4 buffer, DTT / Ionic strength: 25 mM / Label: 15N-PaIF3C / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III6001600 MHZ Bruker Ultra Shield Plus NMR spectrometer
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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