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- PDB-6af3: Toxin-Antitoxin module from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 6af3
TitleToxin-Antitoxin module from Streptococcus pneumoniae
Components
  • HigA antitoxin
  • HigB toxin
KeywordsTOXIN / Toxin-Antitoxin complex
Function / homology
Function and homology information


Toxin HigB-like / Phage derived protein Gp49-like (DUF891) / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
Phage-related protein / HTH cro/C1-type domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.803 Å
AuthorsKang, S.M. / Kim, D.H. / Jin, C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)2018R1A2A1A19018526 Korea, Republic Of
CitationJournal: To Be Published
Title: Toxin-Antitoxin module from Streptococcus pneumoniae
Authors: Kang, S.M. / Kim, D.H. / Jin, C.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: HigB toxin
B: HigA antitoxin
C: HigB toxin
D: HigA antitoxin
E: HigB toxin
F: HigA antitoxin
G: HigB toxin
H: HigA antitoxin


Theoretical massNumber of molelcules
Total (without water)111,9268
Polymers111,9268
Non-polymers00
Water1,09961
1
A: HigB toxin
B: HigA antitoxin
G: HigB toxin
H: HigA antitoxin


Theoretical massNumber of molelcules
Total (without water)55,9634
Polymers55,9634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-40 kcal/mol
Surface area21400 Å2
MethodPISA
2
C: HigB toxin
D: HigA antitoxin
E: HigB toxin
F: HigA antitoxin


Theoretical massNumber of molelcules
Total (without water)55,9634
Polymers55,9634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-49 kcal/mol
Surface area20810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.575, 67.038, 87.717
Angle α, β, γ (deg.)90.00, 94.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HigB toxin


Mass: 16981.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: higB / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UQ08
#2: Protein
HigA antitoxin


Mass: 10999.912 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria)
Strain: TIGR4 / Gene: higA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2UQ20
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) PEG 1000, 0.1M potassium phosphate monobasic/sodium phosphate dibasic, pH 6.2, 0.2M sodium chloride

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 41486 / % possible obs: 99.9 % / Redundancy: 11 % / Rpim(I) all: 0.043 / Net I/σ(I): 24.8
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 2066 / Rpim(I) all: 0.48

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.803→49.795 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.26
RfactorNum. reflection% reflection
Rfree0.3333 2107 5.09 %
Rwork0.2204 --
obs0.2263 41420 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.803→49.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 0 61 6717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0286764
X-RAY DIFFRACTIONf_angle_d3.1269067
X-RAY DIFFRACTIONf_dihedral_angle_d20.462663
X-RAY DIFFRACTIONf_chiral_restr0.122998
X-RAY DIFFRACTIONf_plane_restr0.0141153
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8035-2.86870.38031380.28912576X-RAY DIFFRACTION98
2.8687-2.94040.34841460.26012646X-RAY DIFFRACTION100
2.9404-3.01990.36831510.26832604X-RAY DIFFRACTION100
3.0199-3.10880.37311370.26752601X-RAY DIFFRACTION100
3.1088-3.20910.42231230.25052679X-RAY DIFFRACTION100
3.2091-3.32380.43691320.24492626X-RAY DIFFRACTION100
3.3238-3.45680.38411320.24492625X-RAY DIFFRACTION100
3.4568-3.61410.29311230.22182636X-RAY DIFFRACTION100
3.6141-3.80460.32681560.21652634X-RAY DIFFRACTION100
3.8046-4.04280.38931350.20152615X-RAY DIFFRACTION100
4.0428-4.35480.32631450.1792645X-RAY DIFFRACTION100
4.3548-4.79270.30091620.1752619X-RAY DIFFRACTION100
4.7927-5.48550.3541230.20732628X-RAY DIFFRACTION100
5.4855-6.90820.421380.27422629X-RAY DIFFRACTION100
6.9082-49.80260.27311660.21762550X-RAY DIFFRACTION98

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