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- PDB-7ab3: Crystal structure of the Escherichia coli toxin-antitoxin system ... -

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Basic information

Entry
Database: PDB / ID: 7ab3
TitleCrystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT S57A)
Components
  • Couple_hipA domain-containing protein
  • HipA_C domain-containing protein
  • Predicted transcriptional regulator, XRE family
KeywordsTOXIN / antitoxin / kinase / HTH / HipA / HipT / HipB / HipS / HipBA / HipBST / bacteria / TrpS / phosphorylation / trans-autophosphorylation
Function / homology
Function and homology information


protein serine/threonine kinase activity / DNA binding / cytosol
Similarity search - Function
: / HipA, N-terminal subdomain 1 / HipA N-terminal domain / HipA-like, C-terminal / HipA-like C-terminal domain / Helix-turn-helix / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
HipA-like C-terminal domain-containing protein / HipA N-terminal subdomain 1 domain-containing protein / Predicted transcriptional regulator, XRE family
Similarity search - Component
Biological speciesEscherichia coli O127:H6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBaerentsen, R.L. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0030646 Denmark
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Biorxiv / Year: 2022
Title: Structural basis for regulation of a tripartite toxin-antitoxin system by dual phosphorylation
Authors: Baerentsen, R.L. / Nielsen, S.V. / Lyngso, J. / Bisiak, F. / Pedersen, J.S. / Gerdes, K. / Sorensen, M.A. / Brodersen, D.E.
History
DepositionSep 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted transcriptional regulator, XRE family
B: Couple_hipA domain-containing protein
C: HipA_C domain-containing protein
D: Predicted transcriptional regulator, XRE family
E: Couple_hipA domain-containing protein
F: HipA_C domain-containing protein


Theoretical massNumber of molelcules
Total (without water)125,9216
Polymers125,9216
Non-polymers00
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-51 kcal/mol
Surface area45400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)281.680, 106.070, 57.560
Angle α, β, γ (deg.)90.000, 90.648, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Predicted transcriptional regulator, XRE family


Mass: 11851.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL98
#2: Protein Couple_hipA domain-containing protein


Mass: 11844.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3786 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL97
#3: Protein HipA_C domain-containing protein


Mass: 39264.273 Da / Num. of mol.: 2 / Mutation: S57A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O127:H6 (strain E2348/69 / EPEC) (bacteria)
Strain: E2348/69 / EPEC / Gene: E2348C_3785 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B7UL96
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.84 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1M BICINE, 8% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.4→49.751 Å / Num. obs: 66119 / % possible obs: 99.9 % / Redundancy: 9.466 % / Biso Wilson estimate: 68.91 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.258 / Rrim(I) all: 0.271 / Χ2: 1.018 / Net I/σ(I): 10.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.463.9351.9840.6748080.3592.28899.3
2.46-2.535.1921.8640.9247530.4522.06399.9
2.53-2.67.6841.631.3746140.6161.747100
2.6-2.687.4941.4121.5844940.6371.517100
2.68-2.777.0361.0362.1443230.7511.11999.8
2.77-2.8710.2822.1743.2542330.8632.277100
2.87-2.9811.812.044.0640560.8992.132100
2.98-3.111.6431.3535.4539090.9391.416100
3.1-3.2411.5110.937.3437670.9620.973100
3.24-3.3911.3980.6669.3936100.9780.698100
3.39-3.5810.6240.43311.9634210.9810.456100
3.58-3.811.380.30515.832410.9920.32100
3.8-4.0611.7320.23319.6630260.9950.243100
4.06-4.3811.5580.17623.2828340.9960.185100
4.38-4.811.2770.13426.7526430.9960.14100
4.8-5.3710.1560.12925.8523600.9960.136100
5.37-6.211.4610.1228.1520760.9960.126100
6.2-7.5911.2550.11229.9617980.9970.118100
7.59-10.7310.040.08633.6413750.9970.09199.9
10.73-49.75110.5180.07737.117780.9950.08198.5

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Processing

Software
NameVersionClassification
BUSTERrefinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XSCALEVERSION Mar 15, 2019 BUILT=20190315data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Emsemble model from 4PU4, 2WIU, 3TPT, 4PU3 and 4PU5

4pu4

2wiu

3tpt

4pu3

4pu5


Resolution: 2.4→49.75 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.251 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 3364 -RANDOM
Rwork0.1994 ---
obs0.2013 66119 99.9 %-
Displacement parametersBiso mean: 88.87 Å2
Baniso -1Baniso -2Baniso -3
1--11.9926 Å20 Å2-4.2848 Å2
2--6.6085 Å20 Å2
3---5.3841 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8150 0 0 474 8624
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088393HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9711379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2918SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1450HARMONIC5
X-RAY DIFFRACTIONt_it8393HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1025SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6399SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.74
X-RAY DIFFRACTIONt_other_torsion19.64
LS refinement shellResolution: 2.4→2.42 Å
RfactorNum. reflection% reflection
Rfree0.2625 59 -
Rwork0.2742 --
obs0.2737 1323 95.89 %
Refinement TLS params.

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)
12.26731.1221-0.20625.53120.13082.02760.08710.09870.03440.0987-0.0158-0.06010.0344-0.0601-0.07130.13180.00240.122-0.1202-0.0027-0.117986.6229-14.903618.8226
24.03832.49541.70754.8423.88185.0823-0.3123-0.32480.4302-0.32480.38850.82920.43020.8292-0.0762-0.0440.19110.2244-0.286-0.0670.1748130.6149-16.823116.0435
32.25630.2090.82140.78230.13271.7880.0619-0.1568-0.0501-0.1568-0.07240.0934-0.05010.09340.01050.0855-0.01050.1862-0.12380.0057-0.1297114.46585.70519.325
43.42231.5639-0.0973.6779-0.39132.7170.0544-0.3578-0.1224-0.35780.2441-0.028-0.1224-0.028-0.29850.12530.01870.0658-0.12130.0507-0.10681.5413-29.7447.9759
57.9383-1.79122.77956.5486-2.780310.36560.10610.9220.73310.9220.06821.07610.73311.0761-0.1744-0.43780.2024-0.3069-0.0793-0.0489-0.1873100.5695-63.637529.3476
60.6385-0.7062-0.48622.55450.9012.06080.04170.15940.35060.1594-0.0376-0.10280.3506-0.1028-0.00410.0718-0.0177-0.0547-0.12210.0115-0.097377.9091-63.749213.3044
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A38 - 107
2X-RAY DIFFRACTION2{ B|* }B2 - 101
3X-RAY DIFFRACTION3{ C|* }C2 - 339
4X-RAY DIFFRACTION4{ D|* }D39 - 107
5X-RAY DIFFRACTION5{ E|* }E2 - 102
6X-RAY DIFFRACTION6{ F|* }F2 - 338

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