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- PDB-5jaa: Crystal structure of the HigBA2 toxin-antitoxin complex -

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Basic information

Entry
Database: PDB / ID: 5jaa
TitleCrystal structure of the HigBA2 toxin-antitoxin complex
Components
  • Antitoxin igA-2
  • Toxin HigB-2
KeywordsTOXIN / toxin-antitoxin system
Function / homologyToxin HigB-2 / RelE toxin of RelE / RelB toxin-antitoxin system / Antitoxin MqsA/HigA-2 / Antitoxin component of bacterial toxin-antitoxin system, MqsA / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / Antitoxin HigA-2 / Toxin HigB-2
Function and homology information
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.993 Å
AuthorsHadzi, S. / Loris, R.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Ribosome-dependent Vibrio cholerae mRNAse HigB2 is regulated by a beta-strand sliding mechanism.
Authors: Hadzi, S. / Garcia-Pino, A. / Haesaerts, S. / Jurenas, D. / Gerdes, K. / Lah, J. / Loris, R.
History
DepositionApr 12, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1May 17, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antitoxin igA-2
B: Antitoxin igA-2
C: Toxin HigB-2
D: Toxin HigB-2


Theoretical massNumber of molelcules
Total (without water)50,0554
Polymers50,0554
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-62 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.000, 119.800, 33.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Antitoxin igA-2


Mass: 11628.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: higA-2, VC_A0469 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KMA5
#2: Protein Toxin HigB-2


Mass: 13398.587 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: higB-2, VC_A0468 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KMA6

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM bicine/Tris pH 8.5; 12.5%(w/v) PEG1000; 12.5%(w/v) PEG3350; 12.5%(w/w) MPD; 30 mM NaF; 30 mM NaBr; 30 mM NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97903 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979031
ReflectionResolution: 2.99→43.854 Å / Num. obs: 18810 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 2.19 % / Biso Wilson estimate: 84.95 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Net I/σ(I): 10.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.99-3.170.5371.64192.5
3.17-3.390.3052.77195
3.39-3.660.1675.9197.2
3.66-4.010.0949.93196.4
4.01-4.480.05914.81193.8
4.48-5.160.04419.35192.1
5.16-6.30.04418.9191.2
6.3-8.820.03123.66189.8
8.82-43.8540.02430.44187

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.993→40.472 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 27.59
RfactorNum. reflection% reflection
Rfree0.2482 546 5 %
Rwork0.1999 --
obs0.2024 10911 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 290.68 Å2 / Biso mean: 96.9903 Å2 / Biso min: 25.94 Å2
Refinement stepCycle: final / Resolution: 2.993→40.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 0 3208
Num. residues----407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033263
X-RAY DIFFRACTIONf_angle_d0.644405
X-RAY DIFFRACTIONf_chiral_restr0.025496
X-RAY DIFFRACTIONf_plane_restr0.002569
X-RAY DIFFRACTIONf_dihedral_angle_d12.8241187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9934-3.29450.35771310.28722490262197
3.2945-3.77090.30171360.23625742710100
3.7709-4.74980.21611370.1842609274699
4.7498-40.47560.22831420.18032692283497
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)
12.54013.3141.8319.12682.7873.0463-0.1296-0.0486-0.2767-0.21580.2233-0.8510.00670.2593-0.19380.3795-0.03650.16830.57350.04810.583950.698847.382544.4934
22.36981.32450.43993.2241.64061.1132-0.30530.21160.77130.17860.06311.14910.0924-0.14290.26740.5281-0.0197-0.0710.72020.07010.604340.883463.311648.1507
36.04963.9702-0.29925.6180.17175.0751-0.3737-0.37610.28090.24490.0167-1.2570.8945-0.1820.23940.69550.0766-0.21920.6538-0.07061.516355.794387.68653.4582
42.85961.63381.16572.54871.02390.429-0.1410.8774-1.3574-1.22930.5212-1.56890.00110.26651.52130.3468-0.17560.33370.20520.1387-0.010837.522525.147532.3773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 104)A3 - 104
2X-RAY DIFFRACTION2chain 'B' and (resid 4 through 104 )B4 - 104
3X-RAY DIFFRACTION3chain 'C' and (resid 0 through 110)C0 - 110
4X-RAY DIFFRACTION4chain 'D' and (resid 2 through 109 )D2 - 109

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