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- PDB-5hy3: Crystal structure of Escherichia coli toxin LsoA in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5hy3
TitleCrystal structure of Escherichia coli toxin LsoA in complex with T4 phage antitoxin Dmd
Components
  • Antitoxin Dmd
  • mRNA endoribonuclease LsoA
KeywordsTOXIN/ANTITOXIN / toxin-antitoxin / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


RNA endonuclease activity / viral process / Hydrolases; Acting on ester bonds
Similarity search - Function
Discriminator of mRNA degradation / Discriminator of mRNA degradation / Bacterial toxin, RNase RnlA/LsoA, N-terminal repeated domain / Bacterial toxin, RNase RnlA/LsoA, DBD domain / RNase LS, bacterial toxin / RNase LS, bacterial toxin DBD domain / RNase LS, bacterial toxin N-terminal
Similarity search - Domain/homology
mRNA endoribonuclease LsoA / Antitoxin Dmd
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsWan, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Mol.Microbiol. / Year: 2016
Title: Structural insights into the inhibition mechanism of bacterial toxin LsoA by bacteriophage antitoxin Dmd
Authors: Wan, H. / Otsuka, Y. / Gao, Z.Q. / Wei, Y. / Chen, Z. / Masuda, M. / Yonesaki, T. / Zhang, H. / Dong, Y.H.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mRNA endoribonuclease LsoA
B: Antitoxin Dmd


Theoretical massNumber of molelcules
Total (without water)46,6592
Polymers46,6592
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-13 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.431, 112.431, 95.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein mRNA endoribonuclease LsoA / Toxin LsoA


Mass: 39622.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: lsoA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O82881, Hydrolases; Acting on ester bonds
#2: Protein Antitoxin Dmd


Mass: 7036.255 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: dmd, 61.5, y02B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P39232

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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: 3.23 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.65M ammonium citrate tribase

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9792 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 11548 / % possible obs: 99.6 % / Redundancy: 15.2 % / Net I/σ(I): 61.93
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 16.8 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 8.39 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-20007.04data reduction
HKL-20007.04data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: SAD
Starting model: the Se-Met derivative of this complex

Resolution: 3.1→39.75 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3017 537 4.76 %random selection
Rwork0.2594 ---
obs0.2615 11286 97.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→39.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 0 0 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112551
X-RAY DIFFRACTIONf_angle_d1.463429
X-RAY DIFFRACTIONf_dihedral_angle_d17.719968
X-RAY DIFFRACTIONf_chiral_restr0.058383
X-RAY DIFFRACTIONf_plane_restr0.008436
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0999-3.41170.40441330.29472681X-RAY DIFFRACTION100
3.4117-3.9050.32841360.29652541X-RAY DIFFRACTION95
3.905-4.91840.29761470.23852678X-RAY DIFFRACTION98
4.9184-39.75360.26781210.25072849X-RAY DIFFRACTION98

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