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- PDB-7ab5: Crystal structure of the Escherichia coli toxin-antitoxin system ... -

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Basic information

Entry
Database: PDB / ID: 7ab5
TitleCrystal structure of the Escherichia coli toxin-antitoxin system HipBST (HipT D233Q)
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 / molecular replacement / Resolution: 2.9 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 1.2May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)125,0326
Polymers125,0326
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9980 Å2
ΔGint-51 kcal/mol
Surface area45770 Å2
Unit cell
Length a, b, c (Å)281.661, 106.467, 57.753
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Predicted transcriptional regulator, XRE family


Mass: 11720.580 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: 11713.165 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: 39082.141 Da / Num. of mol.: 2 / Mutation: D233Q
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.: 5 / 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: 3.47 Å3/Da / Density % sol: 64.63 % / Description: Plate
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M BICINE, 6% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1.5418 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2019
RadiationMonochromator: At 26 m, Si (111), double crystal monochromator, horizontally deflecting, LN2 side-cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→49.86 Å / Num. obs: 73090 / % possible obs: 98.7 % / Redundancy: 3.332 % / Biso Wilson estimate: 77.87 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.223 / Χ2: 0.955 / Net I/σ(I): 4.76 / Num. measured all: 243549 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.983.3171.4040.6217686545053320.1881.68197.8
2.98-3.063.3541.1420.8417750534552920.2741.36599
3.06-3.153.360.9691.0517289518351460.3621.15999.3
3.15-3.253.3590.771.4216687503549680.4970.92198.7
3.25-3.353.340.6491.7116322494048870.6110.77798.9
3.35-3.473.2960.5192.2215249468446260.6960.62398.8
3.47-3.63.2970.4192.7214953460845350.7970.50398.4
3.6-3.753.2780.3553.2714136436343130.8420.42698.9
3.75-3.923.3150.2564.3413824423841700.9190.30798.4
3.92-4.113.2980.25.3113107401239740.9520.23999.1
4.11-4.333.2590.1666.4112281380937680.960.19998.9
4.33-4.593.2420.147.5411611361335810.970.16899.1
4.59-4.913.40.1178.9711438340033640.9810.13998.9
4.91-5.33.4320.1248.6910858319031640.9780.14799.2
5.3-5.813.4120.1268.599870292828930.9770.1598.8
5.81-6.493.3860.1268.628738261425810.9750.1598.7
6.49-7.53.3410.1099.567540230022570.9790.1398.1
7.5-9.183.380.07713.036560197019410.990.09298.5
9.18-12.993.4110.05317.35075150214880.9950.06399.1
12.99-49.863.1790.0518.1925758438100.9940.06196.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.9 Å70.41 Å
Translation2.9 Å70.41 Å

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
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: PBD-code from depostion entry D_1292109701

Resolution: 2.9→49.86 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1913 5.07 %RANDOM
Rwork0.193 35784 --
obs0.1947 37697 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 271 Å2 / Biso mean: 89.9688 Å2 / Biso min: 37.63 Å2
Refinement stepCycle: final / Resolution: 2.9→49.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8178 0 0 5 8183
Biso mean---59.26 -
Num. residues----1015
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.980.33311190.32122513263299
2.98-3.060.34571440.308525522696100
3.06-3.150.3651640.301224902654100
3.15-3.250.33991320.294425682700100
3.25-3.370.30821410.283225462687100
3.37-3.50.32611340.254825472681100
3.5-3.660.31221450.22225372682100
3.66-3.850.23931340.199325782712100
3.85-4.090.25991160.182925662682100
4.09-4.410.1711480.161125372685100
4.41-4.850.17081380.142325762714100
4.85-5.550.16391440.149125432687100
5.55-6.990.21361050.185226182723100
7-49.860.18491490.15812613276299
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)
18.0659-4.95164.72474.7035-4.62894.5453-0.11060.30680.0467-0.3291-0.603-1.3070.35781.1290.40850.72840.09110.16470.62680.00831.029594.6978-27.31789.1228
25.86973.90031.02593.60233.31587.5051-0.7630.6152-0.5574-1.66161.2079-1.3560.31120.1977-0.36220.5841-0.04840.11250.551-0.0290.597685.5363-32.66414.1779
35.59852.9364-2.66124.1372-1.08116.9114-0.04110.6290.1445-0.34810.28720.7613-0.3521-0.0970.04050.5523-0.0746-0.04520.5901-0.07270.585272.043-37.41837.6549
43.13712.2386-3.60688.4909-2.06997.11280.44691.1882.166-0.84080.35460.8775-0.6592-0.9135-0.80460.66450.0559-0.07170.5640.1270.714875.2169-27.50673.6043
56.88653.870.67022.4792-1.04656.30650.18330.21740.65930.1431-0.53950.4854-0.7204-0.03110.31590.5420.02260.07340.49620.03920.606579.4738-25.633211.8924
69.74653.0612.2167.84751.69517.9552-0.5572-0.063-1.06240.92960.6729-0.80230.391.0945-0.03610.51150.0538-0.07750.5707-0.03320.548590.2846-29.084916.8098
74.2145-2.6244-0.53144.16760.65547.1558-0.0007-1.133-0.03240.88120.5046-1.46870.6951.7845-0.50870.87110.1249-0.33661.9752-0.10861.3177106.2737-59.326131.4706
88.2406-1.9998-0.41425.6833-3.49547.68660.6559-1.5334-0.32981.32650.5327-0.7075-0.38661.8244-0.99920.84380.0109-0.20971.2604-0.2870.947597.7862-55.657831.9213
94.09513.2965-0.04125.05244.68379.31740.0963-0.6628-0.73490.4752-0.5905-0.13331.01111.06490.50441.78840.257-0.55251.40170.10171.340390.6947-76.645824.0275
106.95660.16983.41692.72263.43495.80241.52050.0161-0.31650.6222-0.32420.6210.48830.4869-1.42062.76880.4383-0.1682.07920.52182.369896.3857-78.149132.9541
114.523-3.86283.1145.3989-2.88932.16830.3344-0.74640.08260.3314-0.38940.34731.18871.93580.23770.97780.2647-0.24461.3587-0.0071.0251102.1807-67.999424.0776
126.6457-1.23591.0725.230.30825.32840.27160.3543-0.4302-0.2413-0.0064-0.4060.59430.6427-0.24990.55750.0851-0.00460.4166-0.13480.640986.7307-74.50713.909
132.2522-0.7026-0.34263.48671.64483.5268-0.04680.0238-0.14130.23970.00160.04260.3618-0.02160.06190.4928-0.0321-0.040.38360.02440.380774.8045-60.584716.6167
148.318-2.76811.65892.4741.22182.3677-0.2085-0.8603-0.29241.77540.3716-0.20990.79040.4122-0.7760.7434-0.0672-0.14720.7480.04830.690590.7548-27.611522.7392
155.99375.75813.01488.41321.83719.62531.0862-0.9232-0.24161.9857-0.6422-0.3207-0.3066-0.0397-0.410.7011-0.02730.01440.4629-0.0030.571488.9863-16.160324.6459
168.83114.0761.2626.32120.09617.06190.00730.80351.6915-0.0091-0.35160.3861-1.2468-0.69620.2490.77520.04420.14230.57740.15460.669388.255-3.600916.9193
177.12683.5626-2.97819.4783-6.62654.70840.0022-0.108-0.30410.60460.92941.6838-0.4105-1.2313-0.64610.71960.08960.070.5740.00680.823479.9882-10.879519.7029
186.55664.71180.83286.24792.79026.5543-0.16090.42180.484-0.41730.17640.2690.30370.36460.06690.71780.06380.14460.42360.06910.750583.7909-16.942213.7549
196.3383.36881.21573.47254.5689.4377-0.00241.1706-0.55190.21390.5022-2.20420.67360.4638-0.38020.55920.08830.10270.6042-0.010.706893.4123-24.74214.852
203.36190.014-0.16916.11183.53699.9409-0.1320.2491-1.27640.31790.2149-1.58870.99251.6880.12670.88580.24330.15890.8985-0.04071.4509131.6722-22.861415.4381
212.61284.1071-0.38447.7586-1.30782.5482-0.145-0.2109-0.8724-0.1047-0.0307-0.79511.1770.68940.22490.89760.13590.010.8342-0.06091.2588123.9825-20.651313.0734
227.71294.52612.53447.37424.20777.0506-0.17350.0824-2.6138-0.9367-0.0144-1.65760.65420.34120.11110.83220.12690.05660.8974-0.0751.3869137.8846-0.229919.6401
233.12060.38824.88287.95572.75298.2781-0.75350.3648-0.3671-1.4826-0.4763-1.7967-2.75952.66480.96741.3227-0.2424-0.00321.4305-0.29321.7603139.1991-10.055614.083
246.40086.79541.71677.7937-0.27367.93640.0568-1.0689-0.36430.6021-0.2576-0.08690.69080.5508-0.2080.72260.2108-0.10430.833-0.07440.9796130.5738-16.075723.7995
255.0837-1.14830.03976.01190.9464.01470.1217-0.3674-0.20240.0771-0.1717-0.1197-0.22140.4025-0.02220.5358-0.069-0.05370.6511-0.00570.4337122.85797.690533.7082
263.1110.21111.27731.53630.27751.95390.03120.2003-0.0922-0.21-0.0547-0.11450.06760.21180.0430.63370.01350.15470.49620.01210.4976112.15033.317614.7726
273.8771-0.24446.0234.84930.34029.8417-0.2546-0.03890.4181-0.4762-0.11680.2644-0.77870.06920.44410.71490.03480.0910.6166-0.04630.6238107.319918.451714.5792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 44 )A38 - 44
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 59 )A45 - 59
3X-RAY DIFFRACTION3chain 'A' and (resid 60 through 70 )A60 - 70
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 83 )A71 - 83
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 98 )A84 - 98
6X-RAY DIFFRACTION6chain 'A' and (resid 99 through 107 )A99 - 107
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 33 )B2 - 33
8X-RAY DIFFRACTION8chain 'B' and (resid 34 through 60 )B34 - 60
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 71 )B61 - 71
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 82 )B72 - 82
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 101 )B83 - 101
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 86 )C2 - 86
13X-RAY DIFFRACTION13chain 'C' and (resid 87 through 338 )C87 - 338
14X-RAY DIFFRACTION14chain 'D' and (resid 38 through 44 )D38 - 44
15X-RAY DIFFRACTION15chain 'D' and (resid 45 through 59 )D45 - 59
16X-RAY DIFFRACTION16chain 'D' and (resid 60 through 70 )D60 - 70
17X-RAY DIFFRACTION17chain 'D' and (resid 71 through 83 )D71 - 83
18X-RAY DIFFRACTION18chain 'D' and (resid 84 through 98 )D84 - 98
19X-RAY DIFFRACTION19chain 'D' and (resid 99 through 107 )D99 - 107
20X-RAY DIFFRACTION20chain 'E' and (resid 2 through 28 )E2 - 28
21X-RAY DIFFRACTION21chain 'E' and (resid 29 through 63 )E29 - 63
22X-RAY DIFFRACTION22chain 'E' and (resid 64 through 74 )E64 - 74
23X-RAY DIFFRACTION23chain 'E' and (resid 75 through 89 )E75 - 89
24X-RAY DIFFRACTION24chain 'E' and (resid 90 through 101 )E90 - 101
25X-RAY DIFFRACTION25chain 'F' and (resid 2 through 86 )F2 - 86
26X-RAY DIFFRACTION26chain 'F' and (resid 87 through 312 )F87 - 312
27X-RAY DIFFRACTION27chain 'F' and (resid 313 through 341 )F313 - 341

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