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- PDB-6g0z: Crystal structure of GDP bound RbgA from S. aureus -

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Basic information

Entry
Database: PDB / ID: 6g0z
TitleCrystal structure of GDP 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 / 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'-DIPHOSPHATE / Ribosome biogenesis GTPase A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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

Downloads & links

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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)69,5204
Polymers68,6332
Non-polymers8862
Water5,350297
1
A: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7602
Polymers34,3171
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosome biogenesis GTPase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7602
Polymers34,3171
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.932, 77.812, 124.667
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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 1.81 Å3/Da / Density % sol: 32.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate, 0.1 M MES pH 6.0, 35% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.15→48.65 Å / Num. obs: 73381 / % possible obs: 99.79 % / Redundancy: 2 % / Net I/σ(I): 2.45
Reflection shellResolution: 2.15→2.23 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PUJ

1puj


Resolution: 2.15→48.649 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.217 3600 4.91 %
Rwork0.1822 --
obs0.1839 73381 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→48.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 56 297 4989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094776
X-RAY DIFFRACTIONf_angle_d1.2126441
X-RAY DIFFRACTIONf_dihedral_angle_d14.1911819
X-RAY DIFFRACTIONf_chiral_restr0.052711
X-RAY DIFFRACTIONf_plane_restr0.006812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17830.31451510.28432697X-RAY DIFFRACTION100
2.1783-2.20810.28271290.26732704X-RAY DIFFRACTION100
2.2081-2.23970.29811380.26132659X-RAY DIFFRACTION100
2.2397-2.27310.27351330.24332708X-RAY DIFFRACTION100
2.2731-2.30860.33621310.24142688X-RAY DIFFRACTION100
2.3086-2.34650.2421560.23672644X-RAY DIFFRACTION100
2.3465-2.38690.28091360.23382701X-RAY DIFFRACTION100
2.3869-2.43030.26311440.22722672X-RAY DIFFRACTION100
2.4303-2.47710.24231400.21242696X-RAY DIFFRACTION100
2.4771-2.52760.21461440.20652654X-RAY DIFFRACTION100
2.5276-2.58260.2561410.20332695X-RAY DIFFRACTION99
2.5826-2.64270.25771540.20172693X-RAY DIFFRACTION100
2.6427-2.70880.26171540.20162627X-RAY DIFFRACTION100
2.7088-2.7820.21691630.19012682X-RAY DIFFRACTION100
2.782-2.86380.23211470.18042683X-RAY DIFFRACTION100
2.8638-2.95630.26971430.19062629X-RAY DIFFRACTION100
2.9563-3.06190.27261390.18332714X-RAY DIFFRACTION100
3.0619-3.18450.20961350.19532685X-RAY DIFFRACTION100
3.1845-3.32940.2237910.19292721X-RAY DIFFRACTION100
3.3294-3.50490.22451420.18032694X-RAY DIFFRACTION100
3.5049-3.72440.22831220.16972719X-RAY DIFFRACTION100
3.7244-4.01180.22321230.15472692X-RAY DIFFRACTION100
4.0118-4.41530.17361320.14332689X-RAY DIFFRACTION100
4.4153-5.05360.15971500.14232657X-RAY DIFFRACTION99
5.0536-6.36480.18641400.17462688X-RAY DIFFRACTION100
6.3648-48.66110.15851220.15492690X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.34160.8786-1.4911.1861-0.38971.81370.2193-0.63370.06690.0474-0.19210.0776-0.02440.15540.0010.1883-0.005-0.03180.1912-0.0120.1312-45.658933.5225138.4104
23.97980.7785-1.82341.0615-0.32151.99280.2233-0.52860.0488-0.0045-0.09760.0598-0.00120.0890.00920.2078-0.0247-0.03190.17640.05110.1445-45.561373.1168144.2118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain B and resseq 2:292)
2X-RAY DIFFRACTION2(chain A and resseq 2:292)

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