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- PDB-6g12: Crystal structure of GMPPNP bound RbgA from S. aureus -

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Basic information

Entry
Database: PDB / ID: 6g12
TitleCrystal structure of GMPPNP bound RbgA from S. aureus
ComponentsRibosome biogenesis GTPase A
KeywordsRNA BINDING PROTEIN / cpGTPase
Function / homology
Function and homology information


ribosome biogenesis / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ribosome biogenesis GTPase A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: Ribosome biogenesis GTPase A
B: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6784
Polymers68,6332
Non-polymers1,0442
Water5,873326
1
A: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8392
Polymers34,3171
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8392
Polymers34,3171
Non-polymers5221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.899, 77.710, 124.360
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: 34316.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: SAUSA300_1136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2XK72
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium fluoride, 0.1 M MES pH 6.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97903 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.929→62.245 Å / Num. obs: 99071 / % possible obs: 99.5 % / Redundancy: 2 % / Net I/σ(I): 6.36
Reflection shellResolution: 1.93→2 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: 1.929→62.245 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91
RfactorNum. reflection% reflection
Rfree0.2559 4884 4.93 %
Rwork0.2268 --
obs0.2283 99071 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.929→62.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 64 326 5026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084786
X-RAY DIFFRACTIONf_angle_d1.1196461
X-RAY DIFFRACTIONf_dihedral_angle_d13.921823
X-RAY DIFFRACTIONf_chiral_restr0.047711
X-RAY DIFFRACTIONf_plane_restr0.006814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.929-1.95090.43291790.38723125X-RAY DIFFRACTION98
1.9509-1.97390.39831570.38713185X-RAY DIFFRACTION98
1.9739-1.9980.38191460.36493215X-RAY DIFFRACTION99
1.998-2.02330.37071510.3583101X-RAY DIFFRACTION98
2.0233-2.04990.38581690.35413167X-RAY DIFFRACTION98
2.0499-2.0780.39181530.34443097X-RAY DIFFRACTION97
2.078-2.10770.35711300.32343165X-RAY DIFFRACTION97
2.1077-2.13910.34051490.31643138X-RAY DIFFRACTION97
2.1391-2.17250.34961420.30833122X-RAY DIFFRACTION96
2.1725-2.20820.29571410.30113085X-RAY DIFFRACTION94
2.2082-2.24620.27071390.28973101X-RAY DIFFRACTION97
2.2462-2.28710.3011670.28343150X-RAY DIFFRACTION98
2.2871-2.33110.29121690.27053161X-RAY DIFFRACTION98
2.3311-2.37870.24691580.2663156X-RAY DIFFRACTION98
2.3787-2.43040.35421780.26043136X-RAY DIFFRACTION98
2.4304-2.48690.28081850.25013159X-RAY DIFFRACTION98
2.4869-2.54910.291670.25193117X-RAY DIFFRACTION98
2.5491-2.6180.32131590.25683126X-RAY DIFFRACTION98
2.618-2.69510.33741530.23823106X-RAY DIFFRACTION96
2.6951-2.78210.25622080.22223131X-RAY DIFFRACTION98
2.7821-2.88150.22631880.20953166X-RAY DIFFRACTION99
2.8815-2.99690.24961810.20813140X-RAY DIFFRACTION99
2.9969-3.13330.26131410.22543194X-RAY DIFFRACTION99
3.1333-3.29840.2292000.21423096X-RAY DIFFRACTION98
3.2984-3.50510.24071400.20653137X-RAY DIFFRACTION97
3.5051-3.77570.19911630.1923178X-RAY DIFFRACTION98
3.7757-4.15560.22551370.17013180X-RAY DIFFRACTION99
4.1556-4.75670.18361680.15483138X-RAY DIFFRACTION98
4.7567-5.99220.21670.16353109X-RAY DIFFRACTION97
5.9922-62.27720.19711990.1673106X-RAY DIFFRACTION98

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