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- PDB-6kmq: 2.3 Angstrom resolution structure of dimeric HigBA toxin-antitoxi... -

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Basic information

Entry
Database: PDB / ID: 6kmq
Title2.3 Angstrom resolution structure of dimeric HigBA toxin-antitoxin complex from E. coli
Components
  • Antitoxin HigA
  • mRNA interferase toxin HigB
KeywordsTOXIN/ANTITOXIN / Toxin-antitoxin complex / HigBA / endoribonuclease / protein-protein complex / PROTEIN BINDING
Function / homology
Function and homology information


toxin-antitoxin complex / regulation of growth / core promoter sequence-specific DNA binding / regulation of mRNA stability / RNA endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of translation / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding
Similarity search - Function
Toxin-antitoxin system, mRNA interferase HigB / HigB_toxin, RelE-like toxic component of a toxin-antitoxin system / Antitoxin HigA / 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
mRNA interferase toxin HigB / Antitoxin HigA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsJadhav, P. / Sinha, V.K. / Rothweiler, U. / Singh, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India) India
CitationJournal: Biochem.J. / Year: 2020
Title: 2.09 angstrom Resolution structure of E. coli HigBA toxin-antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin.
Authors: Jadhav, P.V. / Sinha, V.K. / Chugh, S. / Kotyada, C. / Bachhav, D. / Singh, R. / Rothweiler, U. / Singh, M.
History
DepositionJul 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA interferase toxin HigB
B: Antitoxin HigA


Theoretical massNumber of molelcules
Total (without water)28,6852
Polymers28,6852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-16 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.960, 48.270, 56.070
Angle α, β, γ (deg.)90.000, 100.820, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13676.759 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: higB, ygjN, b3083, JW3054 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P64578, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin HigA


Mass: 15008.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: higA, ygjM, b3082, JW3053 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P67701

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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: 1.76 Å3/Da / Density % sol: 30.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.05M MgCl2, 0.2M KCl, 0.1M Tris pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.3→28.492 Å / Num. obs: 8815 / % possible obs: 97.5 % / Redundancy: 3.75 % / CC1/2: 0.999 / Net I/σ(I): 13.16
Reflection shellResolution: 2.3→2.309 Å / Num. unique obs: 1421 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFG

5ifg


Resolution: 2.35→28.492 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 38.48
RfactorNum. reflection% reflection
Rfree0.2975 420 5.12 %
Rwork0.2604 --
obs0.2621 8201 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 121.36 Å2 / Biso mean: 67.778 Å2 / Biso min: 36.22 Å2
Refinement stepCycle: final / Resolution: 2.35→28.492 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 0 0 1566
Num. residues----207
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 97 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3502-2.690.39591600.3682568
2.69-3.38820.33271330.31552589
3.3882-28.4920.25791270.22262624
Refinement TLS params.Method: refined / Origin x: 8.7668 Å / Origin y: 1.4319 Å / Origin z: 11.0338 Å
111213212223313233
T0.4693 Å20.0837 Å2-0.0072 Å2-0.5184 Å20.0142 Å2--0.4866 Å2
L1.4093 °20.5668 °2-0.6999 °2-1.8053 °2-0.738 °2--2.943 °2
S-0.0608 Å °-0.3188 Å °-0.1194 Å °0.045 Å °-0.128 Å °-0.0263 Å °0.4371 Å °0.5385 Å °0.1463 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 89
2X-RAY DIFFRACTION1allB23 - 138

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