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- PDB-6qbz: Solution structure of the N-terminal domain of the Staphylococcus... -

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Basic information

Entry
Database: PDB / ID: 6qbz
TitleSolution structure of the N-terminal domain of the Staphylococcus aureus Hibernation Promoting Factor
ComponentsRibosome hibernation promoting factor
KeywordsRIBOSOMAL PROTEIN / Hibernation promoting factor / Staphylococcus aureus / 100S ribosome
Function / homology
Function and homology information


negative regulation of translational elongation / ribosomal small subunit binding / cytosolic small ribosomal subunit
Similarity search - Function
Ribosome hibernation promoting factor, long/plastid / Sigma 54 modulation/S30EA ribosomal protein, C-terminal / Sigma 54 modulation/S30EA ribosomal protein, C-terminal domain superfamily / Sigma 54 modulation/S30EA ribosomal protein C terminus / : / Ribosome hibernation promoting factor/RaiA / Ribosome hibernation promotion factor-like / Sigma 54 modulation protein / S30EA ribosomal protein
Similarity search - Domain/homology
Ribosome hibernation promotion factor / Ribosome hibernation promoting factor
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsUsachev, K.S. / Validov, S.Z. / Khusainov, I.S. / Klochkov, V.V. / Aganov, A.V. / Yusupov, M.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation16-14-10014 Russian Federation
CitationJournal: J.Biomol.Nmr / Year: 2019
Title: Solution structure of the N-terminal domain of the Staphylococcus aureus hibernation promoting factor.
Authors: Usachev, K.S. / Validov, S.Z. / Khusainov, I.S. / Varfolomeev, A.A. / Klochkov, V.V. / Aganov, A.V. / Yusupov, M.M.
History
DepositionDec 25, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome hibernation promoting factor


Theoretical massNumber of molelcules
Total (without water)12,9311
Polymers12,9311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7910 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ribosome hibernation promoting factor / HPF


Mass: 12930.717 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: hpf, raiA, BN1321_170086, BTN44_08780, C0J46_03720, C7Q89_05535, CSC83_13900, CSC87_08515, CV021_09125, EP54_02760, EQ90_03750, ERS072840_01629, HMPREF3211_01097, NCTC10654_00858, NCTC11940_ ...Gene: hpf, raiA, BN1321_170086, BTN44_08780, C0J46_03720, C7Q89_05535, CSC83_13900, CSC87_08515, CV021_09125, EP54_02760, EQ90_03750, ERS072840_01629, HMPREF3211_01097, NCTC10654_00858, NCTC11940_00726, NCTC13131_00825, NCTC13196_00432, NCTC13812_00784, NCTC6133_00902, NCTC7878_03405, NCTC9944_00832, RK64_04495, SAMEA1466939_00154, SAMEA1469870_00863, SAMEA1531701_00565, SAMEA1708664_00330, SAMEA1708674_00592
Plasmid: pGS21A / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: W8USK0, UniProt: Q2G055*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
132isotropic12D 1H-13C HSQC
142isotropic13D 1H-13C NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-99% 15N] N-terminal domain of Hibernation Promoting Factor from Staphylococcus aureus, 90% H2O/10% D2O15N90% H2O/10% D2O
solution20.62 mM [U-99% 13C; U-99% 15N] N-terminal domain of Hibernation Promoting Factor from Staphylococcus aureus, 90% H2O/10% D2O13C, 15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMN-terminal domain of Hibernation Promoting Factor from Staphylococcus aureus[U-99% 15N]1
0.62 mMN-terminal domain of Hibernation Promoting Factor from Staphylococcus aureus[U-99% 13C; U-99% 15N]2
Sample conditionsDetails: PBS buffer (90%H2O+10%D2O) at pH 7.6 with 200 mM NH4Cl concentration
Ionic strength: 200 mM / Label: conditions_1 / pH: 7.6 / Pressure: 1 atm / Temperature: 308 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNprocessing
CcpNmr AnalysisCCPNrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNpeak picking
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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