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- PDB-4p78: HicA3 and HicB3 toxin-antitoxin complex -

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Basic information

Entry
Database: PDB / ID: 4p78
TitleHicA3 and HicB3 toxin-antitoxin complex
Components
  • HicA3 Toxin
  • HicB3 antitoxin
KeywordsTOXIN / Yersinia pestis HicA3-HicB3 system / toxin-antitoxin
Function / homology
Function and homology information


endonuclease activity / sequence-specific DNA binding / mRNA binding / regulation of DNA-templated transcription
Similarity search - Function
Double Stranded RNA Binding Domain - #250 / 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 / Arc-type ribbon-helix-helix ...Double Stranded RNA Binding Domain - #250 / 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 / Arc-type ribbon-helix-helix / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein / Type II toxin-antitoxin system HicA family toxin / Uncharacterized protein / Addiction module toxin, HicA family
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsLi de la Sierra-Gallay, I. / Bibi-Triki, S. / van Tilbeurgh, H. / Lazar, N. / Pradel, E.
CitationJournal: J.Bacteriol. / Year: 2014
Title: Functional and Structural Analysis of HicA3-HicB3, a Novel Toxin-Antitoxin System of Yersinia pestis.
Authors: Bibi-Triki, S. / Li de la Sierra-Gallay, I. / Lazar, N. / Leroy, A. / Van Tilbeurgh, H. / Sebbane, F. / Pradel, E.
History
DepositionMar 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Dec 20, 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: HicB3 antitoxin
B: HicB3 antitoxin
C: HicA3 Toxin
D: HicA3 Toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3905
Polymers47,2984
Non-polymers921
Water2,072115
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-38 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.170, 83.160, 88.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HicB3 antitoxin


Mass: 16334.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YPO3369 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0WBS6, UniProt: A0A5P8YCM0*PLUS
#2: Protein HicA3 Toxin


Mass: 7314.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: YP_0318 / Production host: Escherichia coli (E. coli) / References: UniProt: Q74XS2, UniProt: A0A6B3SYE0*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Crystals were obtained in 2.4 M di-sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.12→41.58 Å / Num. obs: 20448 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.82 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.24
Reflection shellResolution: 2.12→2.24 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.85 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P7D and 1whz

4p7d

1whz


Resolution: 2.12→41.58 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 1023 5 %Random selection
Rwork0.1798 ---
obs0.1817 20446 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 6 115 2507
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082449
X-RAY DIFFRACTIONf_angle_d1.0473297
X-RAY DIFFRACTIONf_dihedral_angle_d12.311934
X-RAY DIFFRACTIONf_chiral_restr0.044346
X-RAY DIFFRACTIONf_plane_restr0.005432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1161-2.22770.28381430.2142704X-RAY DIFFRACTION98
2.2277-2.36720.24851430.19372735X-RAY DIFFRACTION100
2.3672-2.550.20241440.19232727X-RAY DIFFRACTION100
2.55-2.80650.251450.19052753X-RAY DIFFRACTION100
2.8065-3.21250.23571460.1752775X-RAY DIFFRACTION100
3.2125-4.04690.20051480.15862811X-RAY DIFFRACTION100
4.0469-41.5880.19371540.17322918X-RAY DIFFRACTION99

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