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- PDB-6c00: Solution structure of translation initiation factor 1 from Clostr... -

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Basic information

Entry
Database: PDB / ID: 6c00
TitleSolution structure of translation initiation factor 1 from Clostridium difficile
ComponentsTranslation initiation factor IF-1
KeywordsTRANSLATION / translation initiation factor
Function / homology
Function and homology information


translation initiation factor activity / ribosome binding / rRNA binding / cytoplasm
Similarity search - Function
Translation initiation factor IF-1 / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / RNA-binding domain, S1 / Ribosomal protein S1-like RNA-binding domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Translation initiation factor IF-1
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsZhang, Y. / Aguilar, F.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Texas Rio Grande Valley United States
CitationJournal: Biomol.Nmr Assign. / Year: 2019
Title: 1H,13C and15N resonance assignments and structure prediction of translation initiation factor 1 from Clostridium difficile.
Authors: Aguilar, F. / Banaei, N. / Zhang, Y.
History
DepositionDec 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_nmr_software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_software.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model
Revision 1.3May 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-1


Theoretical massNumber of molelcules
Total (without water)9,6571
Polymers9,6571
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5780 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Translation initiation factor IF-1


Mass: 9657.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Gene: infA, CD630_00940 / Production host: Escherichia coli (E. coli) / References: UniProt: Q18CI2

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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
232isotropic13D HN(CA)CB
242isotropic13D CBCA(CO)NH
252isotropic13D HNCO
262isotropic13D HBHA(CO)NH
272isotropic13D H(CCO)NH
282isotropic13D C(CO)NH
393isotropic22D 1H-13C HSQC aliphatic
3103isotropic23D (H)CCH-TOCSY
3113isotropic23D 1H-13C NOESY aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 15N] 15N_pET24bCdIF1, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution21 mM [U-99% 13C; U-99% 15N] 13C_15N_pET24bCdIF1, 90% H2O/10% D2O13C_15N_sample90% H2O/10% D2O
solution31 mM [U-99% 13C; U-99% 15N] 13C_15N_pET24bCdIF1, 100% D2O13C_15N_D2O_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mM15N_pET24bCdIF1[U-99% 15N]1
1 mM13C_15N_pET24bCdIF1[U-99% 13C; U-99% 15N]2
1 mM13C_15N_pET24bCdIF1[U-99% 13C; U-99% 15N]3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.12 M15N_pET24bCdIF15.1 1 atm298 K
20.12 M13C_15N_pET24bCdIF15.1 1 atm298 K
30.12 M13C_15N_D2O_pET24bCdIF15.1 pD1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE7002

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Processing

NMR software
NameDeveloperClassification
xplor-NIHG. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandrarefinement
xplor-NIHG. Marius Clore , Guillermo Bermejo, , John Kuszewski, Charles D. Schwieters, and Nico Tjandrastructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structurea are based on a total of 999 restraints, 854 NOE, 112 dihedral angle restraints, 33 hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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