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- PDB-6af4: Toxin-Antitoxin module from Streptococcus pneumoniae -

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Basic information

Entry
Database: PDB / ID: 6af4
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 / MOLECULAR REPLACEMENT / Resolution: 2.65 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 22, 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

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)110,0508
Polymers110,0508
Non-polymers00
Water79344
1
A: HigB toxin
B: HigA antitoxin
G: HigB toxin
H: HigA antitoxin


Theoretical massNumber of molelcules
Total (without water)55,0254
Polymers55,0254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-41 kcal/mol
Surface area20870 Å2
MethodPISA
2
C: HigB toxin
D: HigA antitoxin
E: HigB toxin
F: HigA antitoxin


Theoretical massNumber of molelcules
Total (without water)55,0254
Polymers55,0254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-39 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.903, 73.403, 98.321
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HigB toxin


Mass: 16747.150 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: 10765.437 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.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.92 %
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: Sep 28, 2016
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: 45671 / % possible obs: 97 % / Redundancy: 3.6 % / Net I/σ(I): 23.7
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AF3

6af3


Resolution: 2.65→30.04 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.21
RfactorNum. reflection% reflection
Rfree0.254 1475 4.95 %
Rwork0.216 --
obs0.218 43865 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.65→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 0 44 6810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066874
X-RAY DIFFRACTIONf_angle_d1.1359214
X-RAY DIFFRACTIONf_dihedral_angle_d14.8952706
X-RAY DIFFRACTIONf_chiral_restr0.0391014
X-RAY DIFFRACTIONf_plane_restr0.0051174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.73550.40341190.34382640X-RAY DIFFRACTION98
2.7355-2.83320.30071340.25682690X-RAY DIFFRACTION100
2.8332-2.94650.29381360.242698X-RAY DIFFRACTION100
2.9465-3.08050.28971420.24252661X-RAY DIFFRACTION100
3.0805-3.24270.29671460.24922662X-RAY DIFFRACTION100
3.2427-3.44560.31481210.24972476X-RAY DIFFRACTION92
3.4456-3.71120.30911300.24332416X-RAY DIFFRACTION89
3.7112-4.08390.25721230.22882135X-RAY DIFFRACTION80
4.0839-4.67290.22011290.17482583X-RAY DIFFRACTION95
4.6729-5.88010.23161510.19572641X-RAY DIFFRACTION98
5.8801-30.0420.191440.17842710X-RAY DIFFRACTION98

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