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- PDB-6kml: 2.09 Angstrom resolution crystal structure of tetrameric HigBA to... -

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Basic information

Entry
Database: PDB / ID: 6kml
Title2.09 Angstrom resolution crystal structure of tetrameric 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 / hydrolase activity / 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: 2.095 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: mRNA interferase toxin HigB
D: Antitoxin HigA


Theoretical massNumber of molelcules
Total (without water)57,3704
Polymers57,3704
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-61 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.378, 85.873, 59.408
Angle α, β, γ (deg.)90.000, 90.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resid 1 through 65 or resid 67 through 138))
21(chain D and (resid 1 through 65 or resid 67 through 138))
12(chain A and ((resid -2 and (name N or name...
22(chain C and (resid -2 through 87 or (resid 88...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPRO(chain B and (resid 1 through 65 or resid 67 through 138))BB1 - 651 - 65
121PHEPHEASPASP(chain B and (resid 1 through 65 or resid 67 through 138))BB67 - 13867 - 138
211METMETPROPRO(chain D and (resid 1 through 65 or resid 67 through 138))DD1 - 651 - 65
221PHEPHEASPASP(chain D and (resid 1 through 65 or resid 67 through 138))DD67 - 13867 - 138
112GLNGLNGLNGLN(chain A and ((resid -2 and (name N or name...AA-212
122GLNGLNTHRTHR(chain A and ((resid -2 and (name N or name...AA-2 - 10012 - 114
132GLNGLNTHRTHR(chain A and ((resid -2 and (name N or name...AA-2 - 10012 - 114
142GLNGLNTHRTHR(chain A and ((resid -2 and (name N or name...AA-2 - 10012 - 114
152GLNGLNTHRTHR(chain A and ((resid -2 and (name N or name...AA-2 - 10012 - 114
212GLNGLNTHRTHR(chain C and (resid -2 through 87 or (resid 88...CC-2 - 8712 - 101
222HISHISHISHIS(chain C and (resid -2 through 87 or (resid 88...CC88102
232GLNGLNGLYGLY(chain C and (resid -2 through 87 or (resid 88...CC-2 - 10212 - 116
242GLNGLNGLYGLY(chain C and (resid -2 through 87 or (resid 88...CC-2 - 10212 - 116
252GLNGLNGLYGLY(chain C and (resid -2 through 87 or (resid 88...CC-2 - 10212 - 116
262GLNGLNGLYGLY(chain C and (resid -2 through 87 or (resid 88...CC-2 - 10212 - 116

NCS ensembles :
ID
1
2

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Components

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


Mass: 13676.759 Da / Num. of mol.: 2
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.: 2
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M KCl, 0.05M Tris-Cl pH 7.5, 0.05M MgCl2, 15% 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: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.09→48.852 Å / Num. obs: 32973 / % possible obs: 97.1 % / Redundancy: 3.449 % / CC1/2: 0.998 / Net I/σ(I): 9.75
Reflection shellResolution: 2.095→2.105 Å / Num. unique obs: 939 / CC1/2: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFG

5ifg


Resolution: 2.095→48.852 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.88
RfactorNum. reflection% reflection
Rfree0.2364 1647 5 %
Rwork0.1952 --
obs0.1973 32963 97.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.93 Å2 / Biso mean: 52.3921 Å2 / Biso min: 28.16 Å2
Refinement stepCycle: final / Resolution: 2.095→48.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 0 197 3970
Biso mean---52.97 -
Num. residues----484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083852
X-RAY DIFFRACTIONf_angle_d0.9315204
X-RAY DIFFRACTIONf_chiral_restr0.055596
X-RAY DIFFRACTIONf_plane_restr0.006663
X-RAY DIFFRACTIONf_dihedral_angle_d6.7422597
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B1206X-RAY DIFFRACTION10.322TORSIONAL
12D1206X-RAY DIFFRACTION10.322TORSIONAL
21A886X-RAY DIFFRACTION10.322TORSIONAL
22C886X-RAY DIFFRACTION10.322TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.095-2.15620.46431300.3621246993
2.1562-2.22580.3371370.3135261097
2.2258-2.30540.32131370.2797259597
2.3054-2.39770.31481380.2461263298
2.3977-2.50680.30231390.2382262898
2.5068-2.6390.26761370.2247263298
2.639-2.80430.26031350.2278257096
2.8043-3.02080.27891400.219265599
3.0208-3.32470.25851390.2069264398
3.3247-3.80560.22611370.1904260496
3.8056-4.7940.17151390.1515263997
4.794-48.8520.19281390.1522263996
Refinement TLS params.Method: refined / Origin x: -112.3483 Å / Origin y: -73.615 Å / Origin z: 130.4975 Å
111213212223313233
T0.3609 Å20.0544 Å2-0.0132 Å2-0.2775 Å20.0181 Å2--0.3138 Å2
L0.5909 °20.293 °2-0.3517 °2-0.5568 °20.0221 °2--0.8867 °2
S0.0457 Å °-0.0166 Å °-0.0226 Å °0.0672 Å °-0.0042 Å °0.0208 Å °0.0231 Å °0.0408 Å °-0.0351 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-2 - 100
2X-RAY DIFFRACTION1allB1 - 138
3X-RAY DIFFRACTION1allC-2 - 102
4X-RAY DIFFRACTION1allD1 - 138
5X-RAY DIFFRACTION1allS1 - 208

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