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- PDB-3q8x: Structure of a toxin-antitoxin system bound to its substrate -

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Basic information

Entry
Database: PDB / ID: 3q8x
TitleStructure of a toxin-antitoxin system bound to its substrate
Components
  • Antidote of epsilon-zeta postsegregational killing system
  • Zeta-toxin
KeywordsTRANSFERASE / Polynucleotide kinase fold / epsilon: antidote zeta: bacterial toxin
Function / homology
Function and homology information


negative regulation of cell killing / UDP-N-acetylglucosamine kinase / toxic substance binding / response to toxic substance / kinase activity / phosphorylation / ATP binding
Similarity search - Function
Bacterial epsilon antitoxin / Bacterial epsilon antitoxin / Helicase, Ruva Protein; domain 3 - #130 / Antitoxin epsilon/PezA domain superfamily / Zeta toxin domain / Zeta toxin / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Bacterial epsilon antitoxin / Bacterial epsilon antitoxin / Helicase, Ruva Protein; domain 3 - #130 / Antitoxin epsilon/PezA domain superfamily / Zeta toxin domain / Zeta toxin / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Toxin zeta / Antitoxin epsilon / Antitoxin epsilon
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsMutschler, H. / Gebhardt, M. / Shoeman, R.L. / Meinhart, A.
CitationJournal: Plos Biol. / Year: 2011
Title: A novel mechanism of programmed cell death in bacteria by toxin-antitoxin systems corrupts peptidoglycan synthesis.
Authors: Mutschler, H. / Gebhardt, M. / Shoeman, R.L. / Meinhart, A.
History
DepositionJan 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 2, 2011Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antidote of epsilon-zeta postsegregational killing system
B: Zeta-toxin
C: Antidote of epsilon-zeta postsegregational killing system
D: Zeta-toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1587
Polymers86,3584
Non-polymers7993
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9160 Å2
ΔGint-65 kcal/mol
Surface area32920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.800, 79.990, 195.170
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 Antidote of epsilon-zeta postsegregational killing system


Mass: 10734.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: epsilon / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6UZC8, UniProt: Q57231*PLUS
#2: Protein Zeta-toxin


Mass: 32444.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54944
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2

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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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2 M sodium acetate, 16% (w/v) PEG1500 and 7% (v/v) MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2010
RadiationMonochromator: fixed-exit Si(111) monomchromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 26528 / Num. obs: 25432 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 26.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 4.1 / % possible all: 86.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNSrefinement
XDSdata scaling
XDSdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1GVN

1gvn


Resolution: 2.7→46.52 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 31.514 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R: 1.016 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26309 1323 5 %RANDOM
Rwork0.20968 ---
obs0.21237 25131 100 %-
all-26528 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.864 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å20 Å2
2--0.54 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.7→46.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 49 0 5816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9827996
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8385709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17825.571289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.172151118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8281530
X-RAY DIFFRACTIONr_chiral_restr0.0770.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024375
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.22603
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24098
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2160
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3881.53655
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.66225802
X-RAY DIFFRACTIONr_scbond_it0.94732493
X-RAY DIFFRACTIONr_scangle_it1.594.52194
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 95 -
Rwork0.306 1814 -
obs--100 %
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)
13.03390.8813-1.45688.5581-1.77925.0427-0.0638-0.1926-0.28290.4071-0.0602-0.2349-0.35450.04640.1241-0.332-0.0152-0.0324-0.28560.0437-0.26164.235728.718325.4636
22.23680.6044-0.56341.85070.58972.07880.0530.1024-0.09890.1440.0246-0.2077-0.37790.2719-0.0776-0.42030.0068-0.0111-0.21730.0156-0.151712.959431.07277.4273
33.8568-1.81211.27664.3271-4.354810.19010.0844-0.115-0.10550.3829-0.1773-0.1522-0.63830.00170.0928-0.12260.02260.0279-0.23260.0074-0.154-4.936932.613338.7432
40.87530.1085-0.68482.2025-0.65455.08420.07330.10390.18720.4531-0.0754-0.0254-0.594-0.03590.00210.07850.02530.0656-0.10830.0445-0.0213-12.40931.997757.312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 87
2X-RAY DIFFRACTION2B3 - 274
3X-RAY DIFFRACTION3C2 - 86
4X-RAY DIFFRACTION4D2 - 272

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