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- PDB-6fgk: Crystal structure of the small alarmone synthethase 2 from Bacill... -

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Basic information

Entry
Database: PDB / ID: 6fgk
TitleCrystal structure of the small alarmone synthethase 2 from Bacillus subtilis
ComponentsGTP pyrophosphokinase YwaC
KeywordsTRANSFERASE / Stringent response / alarmone / SAS2 / RelP
Function / homology
Function and homology information


GTP diphosphokinase / GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / kinase activity / GTP binding / ATP binding
Similarity search - Function
: / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GTP pyrophosphokinase YwaC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsBange, G. / Vogt, M. / Steinchen, W. / Altegoer, F.
CitationJournal: Sci Rep / Year: 2018
Title: Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ.
Authors: Steinchen, W. / Vogt, M.S. / Altegoer, F. / Giammarinaro, P.I. / Horvatek, P. / Wolz, C. / Bange, G.
History
DepositionJan 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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: GTP pyrophosphokinase YwaC
B: GTP pyrophosphokinase YwaC
C: GTP pyrophosphokinase YwaC
D: GTP pyrophosphokinase YwaC


Theoretical massNumber of molelcules
Total (without water)98,5544
Polymers98,5544
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-66 kcal/mol
Surface area38170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.670, 99.920, 122.884
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
GTP pyrophosphokinase YwaC / (p)ppGpp synthase YwaC / Small alarmone synthase 2 / SAS 2


Mass: 24638.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: ywaC, BSU38480, ipa-7d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39583, GTP diphosphokinase

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5, 30% (w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.2→47.28 Å / Num. obs: 16011 / % possible obs: 92.2 % / Redundancy: 4.1 % / CC1/2: 0.98 / Rmerge(I) obs: 0.169 / Net I/σ(I): 3.7
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.572 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1561 / CC1/2: 0.72 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DEC

5dec


Resolution: 3.2→46.281 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.38
RfactorNum. reflection% reflection
Rfree0.3192 794 4.96 %
Rwork0.257 --
obs0.2601 16011 91.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→46.281 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 0 0 6058
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046170
X-RAY DIFFRACTIONf_angle_d0.7358309
X-RAY DIFFRACTIONf_dihedral_angle_d3.6423779
X-RAY DIFFRACTIONf_chiral_restr0.052938
X-RAY DIFFRACTIONf_plane_restr0.0051037
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1986-3.3990.36491440.31672471X-RAY DIFFRACTION92
3.399-3.66130.36931260.29912564X-RAY DIFFRACTION93
3.6613-4.02960.4231270.26592521X-RAY DIFFRACTION92
4.0296-4.61220.29941410.24372504X-RAY DIFFRACTION91
4.6122-5.80910.28821100.22682569X-RAY DIFFRACTION91
5.8091-46.28610.26671460.24842588X-RAY DIFFRACTION89

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