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- PDB-6g14: Crystal structure of ppGpp bound RbgA from S. aureus -

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Basic information

Entry
Database: PDB / ID: 6g14
TitleCrystal structure of ppGpp bound RbgA from S. aureus
ComponentsRibosome biogenesis GTPase A
KeywordsRNA BINDING PROTEIN / cpGTPase
Function / homology
Function and homology information


ribosome biogenesis / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...GTPase, MTG1 / GTP-binding protein, ribosome biogenesis / GTP-binding protein, orthogonal bundle domain superfamily / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain / Circularly permuted (CP)-type guanine nucleotide-binding (G) domain profile. / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5',3'-TETRAPHOSPHATE / Ribosome biogenesis GTPase A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPausch, P. / Bange, G.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for (p)ppGpp-mediated inhibition of the GTPase RbgA.
Authors: Pausch, P. / Steinchen, W. / Wieland, M. / Klaus, T. / Freibert, S.A. / Altegoer, F. / Wilson, D.N. / Bange, G.
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Ribosome biogenesis GTPase A
A: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0684
Polymers66,8612
Non-polymers1,2062
Water7,332407
1
B: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0342
Polymers33,4311
Non-polymers6031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0342
Polymers33,4311
Non-polymers6031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.781, 74.512, 125.215
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ribosome biogenesis GTPase A


Mass: 33430.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Gene: SAUSA300_1136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2XK72
#2: Chemical ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp


Type: RNA linking / Mass: 603.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N5O17P4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Potassium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→47.933 Å / Num. obs: 115942 / % possible obs: 99 % / Redundancy: 4.2 % / Net I/σ(I): 7.88
Reflection shellResolution: 1.8→1.864 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G0Z

6g0z


Resolution: 1.8→47.933 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.69
RfactorNum. reflection% reflection
Rfree0.2559 5930 5.11 %
Rwork0.2176 --
obs0.2195 115942 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→47.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 72 407 5020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094697
X-RAY DIFFRACTIONf_angle_d1.1926338
X-RAY DIFFRACTIONf_dihedral_angle_d15.2771792
X-RAY DIFFRACTIONf_chiral_restr0.052694
X-RAY DIFFRACTIONf_plane_restr0.006793
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.40311590.35193403X-RAY DIFFRACTION88
1.8205-1.84190.39472030.32323705X-RAY DIFFRACTION98
1.8419-1.86440.34111810.31363707X-RAY DIFFRACTION97
1.8644-1.8880.35552350.30083681X-RAY DIFFRACTION97
1.888-1.91280.28942490.28423650X-RAY DIFFRACTION97
1.9128-1.9390.28612140.27093654X-RAY DIFFRACTION97
1.939-1.96670.30572100.28273677X-RAY DIFFRACTION97
1.9667-1.99610.31061930.28233667X-RAY DIFFRACTION96
1.9961-2.02720.30142060.2593625X-RAY DIFFRACTION95
2.0272-2.06050.26152040.26153482X-RAY DIFFRACTION93
2.0605-2.0960.28612100.25443448X-RAY DIFFRACTION91
2.096-2.13410.26662230.24253400X-RAY DIFFRACTION90
2.1341-2.17520.27132370.24283729X-RAY DIFFRACTION98
2.1752-2.21960.28642100.233735X-RAY DIFFRACTION99
2.2196-2.26780.25812180.23353728X-RAY DIFFRACTION99
2.2678-2.32060.28672180.22753780X-RAY DIFFRACTION99
2.3206-2.37860.26661980.22893740X-RAY DIFFRACTION99
2.3786-2.44290.28961580.23163793X-RAY DIFFRACTION99
2.4429-2.51480.28622050.22943730X-RAY DIFFRACTION98
2.5148-2.5960.28251920.2213704X-RAY DIFFRACTION97
2.596-2.68880.29011970.24233507X-RAY DIFFRACTION93
2.6888-2.79640.26781340.22663614X-RAY DIFFRACTION92
2.7964-2.92370.29131580.23333784X-RAY DIFFRACTION99
2.9237-3.07780.31651920.22673759X-RAY DIFFRACTION99
3.0778-3.27060.25121930.22373781X-RAY DIFFRACTION99
3.2706-3.5230.25631750.21543796X-RAY DIFFRACTION98
3.523-3.87740.24271620.19853652X-RAY DIFFRACTION96
3.8774-4.43810.18462240.16393590X-RAY DIFFRACTION95
4.4381-5.59020.20311890.16733779X-RAY DIFFRACTION99
5.5902-47.95030.21830.17543712X-RAY DIFFRACTION97

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