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- PDB-8bdv: Ribosome maturation factor P (RimP) from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 8bdv
TitleRibosome maturation factor P (RimP) from Staphylococcus aureus
ComponentsRibosome maturation factor RimP
KeywordsTRANSLATION / Ribosome maturation / Staphylococcus aureus / Ribosome
Function / homology
Function and homology information


ribosomal small subunit biogenesis / cytoplasm
Similarity search - Function
Ribosome maturation factor RimP / Ribosome maturation factor RimP, N-terminal / Ribosome maturation factor RimP, C-terminal / RimP, N-terminal domain superfamily / Ribosome maturation factor RimP, C-terminal domain superfamily / RimP N-terminal domain / RimP C-terminal SH3 domain
Similarity search - Domain/homology
Ribosome maturation factor RimP
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGaraeva, N. / Usachev, K.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Foundation for Basic Research20-34-70021 Russian Federation
CitationJournal: Structure / Year: 2023
Title: Ribosome maturation factor P (RimP) from Staphylococcus aureus
Authors: Garaeva, N. / Usachev, K.
History
DepositionOct 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome maturation factor RimP


Theoretical massNumber of molelcules
Total (without water)17,7201
Polymers17,7201
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
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 maturation factor RimP


Mass: 17720.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: bovine RF122 / ET3-1 / Gene: rimP, SAB1127
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q2YXK3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNHA
121isotropic13D HNHB
1121isotropic13D HBHA(CO)NH
1111isotropic13D HBHAHN
131isotropic13D 15N-1H HSQC-NOESY
142isotropic13D 13C-1H HSQC-NOESY
152isotropic13D HNCA
162isotropic13D HN(CA)CB
172isotropic13D CBCA(CO)NH
1142isotropic13D HN(COCA)CB
182isotropic13D HNCO
192isotropic13D HN(CA)CO
1102isotropic13D HN(CO)CA
1162isotropic12D 1H-13C HSQC
1151isotropic12D 1H-15N HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-99% 15N] Ribosome maturation factor P (RimP), 90% H2O/10% D2O15N90% H2O/10% D2O
solution20.7 mM [U-99% 13C; U-99% 15N] Ribosome maturation factor P (RimP), 90% H2O/10% D2O13C, 15N90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMRibosome maturation factor P (RimP)[U-99% 15N]1
0.7 mMRibosome maturation factor P (RimP)[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 0 Not defined / Label: 250mMNaCl, 10mM Tris-HCl / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
CcpNmr AnalysisCCPNchemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure calculation
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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