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- PDB-7bye: Toxin-antitoxin complex from klebsiella pneumoniae -

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Basic information

Entry
Database: PDB / ID: 7bye
TitleToxin-antitoxin complex from klebsiella pneumoniae
Components
  • Antitoxin MazE
  • Uncharacterized protein
KeywordsHYDROLASE / protein complex
Function / homology
Function and homology information


rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / DNA binding
Similarity search - Function
SpoVT / AbrB like domain / Antidote-toxin recognition MazE, bacterial antitoxin / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / mRNA interferase PemK-like / PemK-like, MazF-like toxin of type II toxin-antitoxin system / Plasmid maintenance toxin/Cell growth inhibitor
Similarity search - Domain/homology
PHOSPHATE ION / Antitoxin MazE / Uncharacterized protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
Klebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKang, S.M.
Funding support1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)
CitationJournal: To Be Published
Title: Toxin-antitoxin complex from klebsiella pneumoniae
Authors: Kang, S.M.
History
DepositionApr 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Antitoxin MazE
B: Uncharacterized protein
C: Uncharacterized protein
D: Antitoxin MazE
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4998
Polymers55,3096
Non-polymers1902
Water1,964109
1
A: Antitoxin MazE
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7494
Polymers27,6543
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-47 kcal/mol
Surface area10300 Å2
MethodPISA
2
D: Antitoxin MazE
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7494
Polymers27,6543
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-39 kcal/mol
Surface area9840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.558, 45.501, 69.952
Angle α, β, γ (deg.)102.060, 93.600, 116.360
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide Antitoxin MazE


Mass: 3607.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: mazE, SAMEA3531848_05753 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C3QI06
#2: Protein
Uncharacterized protein


Mass: 12023.712 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578) (bacteria)
Gene: KPN_pKPN7p10264 / Production host: Escherichia coli (E. coli) / References: UniProt: A6TJ73
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Tris

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 17681 / % possible obs: 89.5 % / Redundancy: 3.2 % / Rpim(I) all: 0.067 / Net I/σ(I): 18.9
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 909 / Rpim(I) all: 0.111

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2323 908 -
Rwork0.1982 --
obs-17676 89.08 %
Displacement parametersBiso mean: 25.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 10 111 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00743592
X-RAY DIFFRACTIONf_angle_d1.18364884
X-RAY DIFFRACTIONf_chiral_restr0.0562601
X-RAY DIFFRACTIONf_plane_restr0.0054616
X-RAY DIFFRACTIONf_dihedral_angle_d11.06282171
LS refinement shellResolution: 2.3→2.34 Å /
Num. reflection% reflection
obs909 91.2 %

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