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- PDB-6zhl: Crystal Structure of Staphylococcus aureus RsgA bound to ppGpp. -

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Basic information

Entry
Database: PDB / ID: 6zhl
TitleCrystal Structure of Staphylococcus aureus RsgA bound to ppGpp.
ComponentsSmall ribosomal subunit biogenesis GTPase RsgA
KeywordsRNA BINDING PROTEIN / GTPase / ppGpp-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',3'-TETRAPHOSPHATE / TRIETHYLENE GLYCOL / Small ribosomal subunit biogenesis GTPase RsgA
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 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 1.1Jan 12, 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)37,36511
Polymers36,1121
Non-polymers1,25310
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint23 kcal/mol
Surface area13800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.450, 66.929, 114.158
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
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / 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, 108 molecules

#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.67 Å3/Da / Density % sol: 53.91 % / Description: Clusters of rod-shaped crystals
Crystal growTemperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium Citrate, 0.1 M Bis-Tris Propane pH 6.5, 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 XE 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: 1.94→57.74 Å / Num. obs: 29355 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.046 / Rrim(I) all: 0.165 / Net I/σ(I): 11
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
1.94-1.9912.70.952679621150.8020.2760.992.599.5
8.68-57.7310.70.04542794000.9980.0140.04834.899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimless0.6.2data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T9H

1t9h


Resolution: 1.94→57.73 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 4.633 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2622 1464 5 %RANDOM
Rwork0.2139 ---
obs0.2163 27838 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.9 Å2 / Biso mean: 32.011 Å2 / Biso min: 13.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---1 Å20 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 1.94→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2185 0 75 98 2358
Biso mean--42.69 30.38 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192345
X-RAY DIFFRACTIONr_bond_other_d0.0020.022149
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9743142
X-RAY DIFFRACTIONr_angle_other_deg1.0834983
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3165269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.11824.472123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9315400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2071515
X-RAY DIFFRACTIONr_chiral_restr0.1110.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022525
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02478
LS refinement shellResolution: 1.94→1.99 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3 104 -
Rwork0.322 1976 -
obs--97.65 %

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