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- PDB-9hlo: AbiEi (antitoxin) AbiEii (toxin) toxin-antitoxin heterodimer comp... -

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Basic information

Entry
Database: PDB / ID: 9hlo
TitleAbiEi (antitoxin) AbiEii (toxin) toxin-antitoxin heterodimer complex from Streptococcus agalactiae
Components
  • Abortive infection protein AbiGI
  • Abortive infection protein AbiGII
KeywordsTOXIN / antitoxin / complex / nucleotidyltransferase
Function / homology
Function and homology information


DNA-binding transcription repressor activity / protein-DNA complex / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription
Similarity search - Function
Transcriptional regulator, AbiEi antitoxin / Transcriptional regulator, AbiEi antitoxin / Nucleotidyl transferase AbiEii toxin, Type IV TA system / Nucleotidyl transferase AbiEii toxin, Type IV TA system
Similarity search - Domain/homology
: / Abortive infection protein AbiGII / Abortive infection protein AbiGI
Similarity search - Component
Biological speciesStreptococcus agalactiae 2603V/R (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsArrowsmith, T.J. / Blower, T.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S022791/1 United Kingdom
CitationJournal: To Be Published
Title: AbiEi:AbiEii heterodimer
Authors: Arrowsmith, T.J. / Blower, T.R.
History
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Abortive infection protein AbiGI
B: Abortive infection protein AbiGII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6933
Polymers56,3802
Non-polymers3121
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.355, 86.796, 85.245
Angle α, β, γ (deg.)90.00, 118.27, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Abortive infection protein AbiGI


Mass: 23101.580 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria)
Strain: 2603 V/R / Gene: abiGI, SAG1284 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q8DZ36
#2: Protein Abortive infection protein AbiGII


Mass: 33278.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae 2603V/R (bacteria)
Strain: 2603 V/R / Gene: abiGII, SAG1285 / Production host: Escherichia coli (E. coli) / Variant (production host): ER2566 / References: UniProt: Q8DZ35
#3: Chemical ChemComp-A1IVY / Pentaerythritol ethoxylate (15/4 EO/OH) / 2-[3-(2-hydroxyethyloxy)-2,2-bis(2-hydroxyethyloxymethyl)propoxy]ethanol


Mass: 312.357 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H28O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2 M potassium acetate, 0.1 M MES pH 6.0, 15% v/v pentaerythritol ethoxyloate (15/4 EO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 15, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→72.784 Å / Num. obs: 27558 / % possible obs: 99.99 % / Redundancy: 2 % / Biso Wilson estimate: 46.31 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.014 / Rrim(I) all: 0.02 / Χ2: 0.26 / Net I/σ(I): 26.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2757 / CC1/2: 0.991 / Rrim(I) all: 0.105 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→72.784 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2737 1975 7.17 %
Rwork0.2277 --
obs0.2311 27558 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→72.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3805 0 21 111 3937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083899
X-RAY DIFFRACTIONf_angle_d0.9455254
X-RAY DIFFRACTIONf_dihedral_angle_d20.091469
X-RAY DIFFRACTIONf_chiral_restr0.053595
X-RAY DIFFRACTIONf_plane_restr0.005653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.3641330.2641813X-RAY DIFFRACTION100
2.255-2.3160.31461400.25831802X-RAY DIFFRACTION100
2.316-2.38420.34661470.2641825X-RAY DIFFRACTION100
2.3842-2.46110.3071450.26431833X-RAY DIFFRACTION100
2.4611-2.54910.3191340.2541827X-RAY DIFFRACTION100
2.5491-2.65110.30971400.25791828X-RAY DIFFRACTION100
2.6511-2.77180.35141380.25421799X-RAY DIFFRACTION100
2.7718-2.91790.30071390.25291850X-RAY DIFFRACTION100
2.9179-3.10080.30191380.27461812X-RAY DIFFRACTION100
3.1008-3.34020.34241410.24711816X-RAY DIFFRACTION100
3.3402-3.67630.26731450.2361832X-RAY DIFFRACTION100
3.6763-4.20820.27511360.20221834X-RAY DIFFRACTION100
4.2082-5.30170.19491500.1871842X-RAY DIFFRACTION100
5.3017-72.7840.24261490.20631870X-RAY DIFFRACTION100

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