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- PDB-6zhm: Crystal Structure of Staphylococcus aureus RsgA bound to GDP. -

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Basic information

Entry
Database: PDB / ID: 6zhm
TitleCrystal Structure of Staphylococcus aureus RsgA bound to GDP.
ComponentsSmall ribosomal subunit biogenesis GTPase RsgA
KeywordsRNA BINDING PROTEIN / GTPase / GDP-binding / TRAFAC / ribosome assembly
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / ribosomal small subunit biogenesis / rRNA binding / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribosome biogenesis GTPase RsgA, N-terminal / RsgA N-terminal domain / Ribosome biogenesis GTPase RsgA / RsgA GTPase domain / RsgA GTPase / EngC GTPase domain profile. / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / TRIETHYLENE GLYCOL / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 3, 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 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,8956
Polymers36,1121
Non-polymers7835
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint4 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.240, 66.970, 113.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Small ribosomal subunit biogenesis GTPase RsgA


Mass: 36111.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: V(-5) as labelled here should be taken as V1, as this is the true initiating codon in this instance.
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Gene: rsgA, SAUSA300_1114 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2XJQ2, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.64 Å3/Da / Density % sol: 53.42 % / Description: Cluster of rod-shaped crystals
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium Citrate, 0.1 M Bis-Tris Propane, 20% w/v PEG 3350

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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: 2.15→101.94 Å / Num. obs: 37173 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.259 / Rpim(I) all: 0.109 / Rrim(I) all: 0.282 / Net I/σ(I): 5.5 / Num. measured all: 239084 / Scaling rejects: 1
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
2.15-2.266.12.1283305553780.3750.9092.32199.6
6.79-101.946.20.096777012570.9940.040.10415.499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZHL

6zhl


Resolution: 2.15→101.94 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.2727 --RANDOM
Rwork0.24 ---
obs-37173 99.9 %-
Displacement parametersBiso max: 91.43 Å2 / Biso mean: 39.697 Å2 / Biso min: 7.57 Å2
Refinement stepCycle: LAST / Resolution: 2.15→101.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 47 111 2337

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