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- PDB-6hpb: Crystal structure of the E.coli HicAB toxin-antitoxin complex -

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Basic information

Entry
Database: PDB / ID: 6hpb
TitleCrystal structure of the E.coli HicAB toxin-antitoxin complex
Components
  • Antitoxin HicB
  • mRNA interferase toxin HicA
KeywordsTOXIN / toxin-antitoxin / TA / protein complex / DNA-binding / TA complex
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / mRNA binding / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HicA mRNA interferase family / HicA superfamily / HicA toxin of bacterial toxin-antitoxin, / HicB-like antitoxin of toxin-antitoxin system / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Antitoxin HicB / Probable mRNA interferase toxin HicA
Similarity search - Component
Biological speciesEscherichia coli str. K-12 substr. MG1655 (bacteria)
Escherichia coli 2-222-05_S4_C3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsManav, M.C. / Brodersen, D.E.
Funding support Denmark, 2items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0030646 Denmark
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Structure / Year: 2019
Title: The E. coli HicB Antitoxin Contains a Structurally Stable Helix-Turn-Helix DNA Binding Domain.
Authors: Manav, M.C. / Turnbull, K.J. / Jurenas, D. / Garcia-Pino, A. / Gerdes, K. / Brodersen, D.E.
History
DepositionSep 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA interferase toxin HicA
B: Antitoxin HicB
C: mRNA interferase toxin HicA
D: Antitoxin HicB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9687
Polymers44,6804
Non-polymers2883
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-68 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.000, 100.000, 88.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11B-387-

HOH

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Components

#1: Protein mRNA interferase toxin HicA / Endoribonuclease HicA / Toxin HicA


Mass: 6890.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria)
Gene: hicA, yncN, b4532, JW5230 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P76106, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin HicB


Mass: 15449.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 2-222-05_S4_C3 (bacteria)
Gene: hicB, ydcQ, b1438, JW1433 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P67697
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M Sodium acetate 4.6 2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.28→62.03 Å / Num. obs: 23248 / % possible obs: 97.54 % / Redundancy: 2 % / Biso Wilson estimate: 79.74 Å2 / Rmerge(I) obs: 0.0551 / Net I/σ(I): 1.5
Reflection shellResolution: 2.28→2.362 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2320 / CC1/2: 0.672 / % possible all: 100

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.28→62.03 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2734 --
Rwork0.2411 --
obs-23243 97.56 %
Displacement parametersBiso mean: 79.74 Å2
Refinement stepCycle: LAST / Resolution: 2.28→62.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 15 153 3204

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