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- PDB-6g26: The crystal structure of the Burkholderia pseudomallei HicAB complex -

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Basic information

Entry
Database: PDB / ID: 6g26
TitleThe crystal structure of the Burkholderia pseudomallei HicAB complex
Components
  • HicA
  • HicB
KeywordsANTITOXIN / N-terminal domain of the antitoxin HicB which acts as an inhibitor to HicA
Function / homology
Function and homology information


hydrolase activity / mRNA binding
Similarity search - Function
Hypothetical protein. / 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 / Metal Transport, Frataxin; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / HicB-like antitoxin of toxin-antitoxin system domain-containing protein / Addiction module toxin, HicA family
Similarity search - Component
Biological speciesBurkholderia pseudomallei K96243 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWinter, A.J. / Isupov, M.N. / Williams, C. / Crump, M.P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J014400/1 United Kingdom
CitationJournal: J Biol Chem / Year: 2018
Title: The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.
Authors: Ashley J Winter / Christopher Williams / Michail N Isupov / Hannah Crocker / Mariya Gromova / Philip Marsh / Oliver J Wilkinson / Mark S Dillingham / Nicholas J Harmer / Richard W Titball / Matthew P Crump /
Abstract: Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which ...Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.
History
DepositionMar 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.3Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: HicB
B: HicB
C: HicB
D: HicB
E: HicA
F: HicA
G: HicA
H: HicA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,06832
Polymers91,3208
Non-polymers1,74824
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, native mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22410 Å2
ΔGint-137 kcal/mol
Surface area35720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.140, 74.190, 85.310
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D
17E
27F
18E
28G
19E
29H
110F
210G
111F
211H
112G
212H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 135
2010B1 - 135
1020A1 - 135
2020C1 - 135
1030A1 - 135
2030D1 - 135
1040B1 - 136
2040C1 - 136
1050B1 - 136
2050D1 - 136
1060C1 - 136
2060D1 - 136
1070E-1 - 59
2070F-1 - 59
1080E0 - 58
2080G0 - 58
1090E0 - 58
2090H0 - 58
10100F0 - 58
20100G0 - 58
10110F0 - 58
20110H0 - 58
10120G0 - 59
20120H0 - 59

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
HicB


Mass: 15762.726 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: BPSS0391 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63NA5
#2: Protein
HicA


Mass: 7067.287 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei K96243 (bacteria)
Gene: BPSS0390 / Production host: Escherichia coli (E. coli) / References: UniProt: Q63NA6

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Non-polymers , 4 types, 293 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.89 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5 0.2 M NH4S04 16% (w/v) PEG 5000 MME 25% (v/v) glycerol

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.49→38.15 Å / Num. obs: 35696 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.12 / Net I/σ(I): 14.1
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.246 / CC1/2: 0.655 / Rrim(I) all: 1.349 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G1N

6g1n


Resolution: 2.49→34.02 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.757 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.254
Details: NCS averaging in DM for phase improvement NCS operators for HicA and HicB
RfactorNum. reflection% reflectionSelection details
Rfree0.23254 1722 4.6 %RANDOM
Rwork0.18692 ---
obs0.18905 35696 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.901 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å2-0 Å2-2.59 Å2
2--0.99 Å20 Å2
3----2.93 Å2
Refinement stepCycle: 1 / Resolution: 2.49→34.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 107 269 6465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196537
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.978868
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42723.723274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.853151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1161542
X-RAY DIFFRACTIONr_chiral_restr0.1230.21007
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214845
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it10.06514.0463205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it11.78623.5414009
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it14.19515.9533332
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined16.66325067
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A81200.06
12B81200.06
21A79940.07
22C79940.07
31A80060.07
32D80060.07
41B80600.08
42C80600.08
51B80280.08
52D80280.08
61C80160.08
62D80160.08
71E36320.09
72F36320.09
81E36180.07
82G36180.07
91E33380.11
92H33380.11
101F36140.08
102G36140.08
111F34240.12
112H34240.12
121G34300.12
122H34300.12
LS refinement shellResolution: 2.49→2.555 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 96 -
Rwork0.333 2656 -
obs--99.78 %

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