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- PDB-9dcn: Solution structure of the translation initiation factor IF-1 from... -

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Basic information

Entry
Database: PDB / ID: 9dcn
TitleSolution structure of the translation initiation factor IF-1 from Neisseria gonorrhoeae (NCCP11945). Seattle Structural Genomics Center for Infectious Disease target NegoA.17902.a
ComponentsTranslation initiation factor IF-1
KeywordsRNA BINDING PROTEIN / protein synthesis / translation initiation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / DNA BINDING PROTEIN
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. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Translation initiation factor IF-1
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodSOLUTION NMR / torsion angle dynamics / molecular dynamics
AuthorsBuchko, G.W. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
CitationJournal: To Be Published
Title: Structural characterization of the translation initiation factor IF-1 from Neisseria gonorrhoeae.
Authors: Buchko, G.W. / van Voorhis, W.C. / Craig, J. / Myler, P.J.
History
DepositionAug 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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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)9,3401
Polymers9,3401
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a monomer via SEC.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Translation initiation factor IF-1


Mass: 9339.878 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090) (bacteria)
Strain: ATCC 700825 / FA 1090 / Gene: infA, NGO1821.1, NGO18211 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F5U8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-13C HSQC aliphatic
121isotropic12D 1H-15N HSQC
131isotropic13D 1H-13C NOESY aliphatic
141isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY
1121isotropic13D 1H-15N TOCSY
1111isotropic13D C(CO)NH
1101isotropic13D HN(CA)CB
191isotropic13D CBCA(CO)NH
181isotropic13D HNCO
172isotropic12D 1H-15N HSQC Deuterium Exchange
162isotropic12D 1H-13C HSQC aliphatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.8 mM [U-98% 13C; U-98% 15N] R20, 93% H2O/7% D2OR20_CN93% H2O/7% D2O
solution2200 mM sodium chloride, 20 mM TRIS, 1 mM EDTA, 1 mM DTT, 0.2 mM [U-10% 13C; U-99% 15N] R20, 100% D2OR20_C10100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 mMsodium chloridenatural abundance1
20 mMTRISnatural abundance1
1 mMEDTAnatural abundance1
1 mMDTTnatural abundance1
0.8 mMR20[U-98% 13C; U-98% 15N]1
200 mMsodium chloridenatural abundance2
20 mMTRISnatural abundance2
1 mMEDTAnatural abundance2
1 mMDTTnatural abundance2
0.2 mMR20[U-10% 13C; U-99% 15N]2
Sample conditionsIonic strength: 222 mM / Ionic strength err: 5 / Label: 1 / pH: 7 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5

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NMR measurement

NMR spectrometerType: Bruker Ascend / Manufacturer: Bruker / Model: Ascend / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.2Guntert, Mumenthaler and Wuthrichstructure calculation
CNSSOLVE 1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
PokyManthey, Tonelli, Clos II, Rahimi, Markley and Leechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxdata analysis
Refinement
MethodSoftware ordinalDetails
torsion angle dynamics1
molecular dynamics2Water Refinement. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 0% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW. Only 8 slowly exchanging amide resonances observed in the deuterium exchange experiment. Other hydrogen bonds introduced on the basis of proximity in early structure calculations (after addition of dihedral angle restraints).
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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