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- PDB-7ztb: Structure of the Salmonella tRNA pyrophosphokinase CapRel -

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Basic information

Entry
Database: PDB / ID: 7ztb
TitleStructure of the Salmonella tRNA pyrophosphokinase CapRel
ComponentsRelA/SpoT family protein
KeywordsTOXIN / toxin-antitoxin / small alarmone synthetase / tRNA pyrophosphokinase / CapRel / bacterial defence
Function / homologyguanosine tetraphosphate metabolic process / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / Nucleotidyltransferase superfamily / RelA/SpoT family protein
Function and homology information
Biological speciesSalmonella phage SJ46 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 Å
AuthorsGarcia-Pino, A.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS) Belgium
CitationJournal: Nature / Year: 2022
Title: Direct activation of a bacterial innate immune system by a viral capsid protein.
Authors: Zhang, T. / Tamman, H. / Coppieters 't Wallant, K. / Kurata, T. / LeRoux, M. / Srikant, S. / Brodiazhenko, T. / Cepauskas, A. / Talavera, A. / Martens, C. / Atkinson, G.C. / Hauryliuk, V. / ...Authors: Zhang, T. / Tamman, H. / Coppieters 't Wallant, K. / Kurata, T. / LeRoux, M. / Srikant, S. / Brodiazhenko, T. / Cepauskas, A. / Talavera, A. / Martens, C. / Atkinson, G.C. / Hauryliuk, V. / Garcia-Pino, A. / Laub, M.T.
History
DepositionMay 9, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 31, 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: RelA/SpoT family protein
B: RelA/SpoT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7645
Polymers85,6832
Non-polymers813
Water4,089227
1
A: RelA/SpoT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9003
Polymers42,8411
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RelA/SpoT family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8642
Polymers42,8411
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.573, 136.196, 57.782
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RelA/SpoT family protein


Mass: 42841.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella phage SJ46 (virus) / Gene: J46_0058
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A1B0VBT5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 277.16 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: peg 20000, 20%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.312→68.1 Å / Num. obs: 20877 / % possible obs: 91.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 59.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.046 / Rrim(I) all: 0.124 / Net I/σ(I): 11.2
Reflection shellResolution: 2.312→2.61 Å / Rmerge(I) obs: 1.292 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1044 / CC1/2: 0.531

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6S2T

6s2t


Resolution: 2.312→68.1 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.357
RfactorNum. reflection% reflectionSelection details
Rfree0.2648 1065 5.1 %RANDOM
Rwork0.2118 ---
obs0.2145 20877 63.9 %-
Displacement parametersBiso mean: 68.66 Å2
Baniso -1Baniso -2Baniso -3
1--7.6132 Å20 Å21.147 Å2
2--5.0095 Å20 Å2
3---2.6037 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.312→68.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 3 228 5535
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085389HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.977277HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1898SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes910HARMONIC5
X-RAY DIFFRACTIONt_it5389HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.73
X-RAY DIFFRACTIONt_other_torsion18.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion741SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4303SEMIHARMONIC4
LS refinement shellResolution: 2.312→2.5 Å
RfactorNum. reflection% reflection
Rfree0.3287 -5.5 %
Rwork0.2738 395 -
obs--6.29 %
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)
11.13080.3125-0.22710.02140.45380.82420.1029-0.03060.0887-0.0194-0.042-0.01460.0486-0.0357-0.0608-0.1523-0.011-0.01510.06830.02950.0128-8.862913.0971-17.8803
20.7112-0.4546-0.23840.73721.12390.6507-0.07520.07440.00240.24590.00420.06620.3359-0.01920.0710.06430.06610.145-0.07630.0683-0.0478-31.651347.169615.2267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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