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- PDB-6zjo: Crystal Structure of Staphylococcus aureus RsgA. -

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Basic information

Entry
Database: PDB / ID: 6zjo
TitleCrystal Structure of Staphylococcus aureus RsgA.
ComponentsSmall ribosomal subunit biogenesis GTPase RsgA
KeywordsRNA BINDING PROTEIN / GTPase / TRAFAC / ribosome assembly
Function / homologyPHOSPHATE ION / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsBennison, D.J. / Rafferty, J.B. / Corrigan, R.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trusthttps://wellcome.ac.uk:104110/Z/14/Z United Kingdom
Royal Societyhttps://wellcome.ac.uk:104110/Z/14/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/N013840/1 United Kingdom
CitationJournal: Mbio / Year: 2021
Title: The Stringent Response Inhibits 70S Ribosome Formation in Staphylococcus aureus by Impeding GTPase-Ribosome Interactions.
Authors: Bennison, D.J. / Nakamoto, J.A. / Craggs, T.D. / Milon, P. / Rafferty, J.B. / Corrigan, R.M.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Small ribosomal subunit biogenesis GTPase RsgA
B: Small ribosomal subunit biogenesis GTPase RsgA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,63223
Polymers72,2242
Non-polymers1,40921
Water3,819212
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint13 kcal/mol
Surface area26600 Å2
Unit cell
Length a, b, c (Å)54.671, 93.566, 68.177
Angle α, β, γ (deg.)90.000, 90.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Small ribosomal subunit biogenesis GTPase RsgA


Mass: 36111.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A4V5LHH4, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.61 % / Description: A single rod-shaped crystal
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.15 M ammonium sulphate, 0.1 M MES, 15% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 13, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.01→47.2 Å / Num. obs: 44789 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.057 / Rrim(I) all: 0.149 / Net I/σ(I): 8.4 / Num. measured all: 306023 / Scaling rejects: 195
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.0670.8282282732540.5940.3360.8951.897
8.99-47.26.50.03534905350.9990.0150.03838.499.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZHL

6zhl


Resolution: 2.01→47.196 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES :REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2783 --
Rwork0.2241 --
obs-44789 98.2 %
Displacement parametersBiso max: 123.45 Å2 / Biso mean: 40.2119 Å2 / Biso min: 17.89 Å2
Refinement stepCycle: LAST / Resolution: 2.01→47.196 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 81 212 4564

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