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- PDB-9ils: The GmvT toxin in complex with the C-terminal fragment of its ant... -

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Basic information

Entry
Database: PDB / ID: 9ils
TitleThe GmvT toxin in complex with the C-terminal fragment of its antitoxin
Components
  • DUF1778 domain-containing protein
  • N-acetyltransferase
KeywordsTOXIN / toxin-antitoxin system / GNAT / acetylation / AcCoA / GmvAT
Function / homologyPHOSPHATE ION / :
Function and homology information
Biological speciesShigella sonnei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsXie, W. / Chen, R. / Zhao, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Febs Lett. / Year: 2025
Title: Structural insights into the Shigella flexneri GmvAT toxin-antitoxin system.
Authors: Chen, R. / Zhao, H. / Zhou, J. / Liu, A. / Guo, Y. / Wu, K. / Xiang, Y. / Lei, J. / Jiang, S. / Xie, W.
History
DepositionJul 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetyltransferase
B: DUF1778 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9393
Polymers23,8442
Non-polymers951
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-30 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.572, 78.572, 131.937
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein N-acetyltransferase / GmvT


Mass: 18870.719 Da / Num. of mol.: 1 / Mutation: Q100R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella sonnei (bacteria) / Gene: CBL27_26410 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A200L144
#2: Protein/peptide DUF1778 domain-containing protein


Mass: 4973.642 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenBank: UUR52005.1 / Source: (gene. exp.) Shigella sonnei (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.47 Å3/Da / Density % sol: 50.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.4-1.9 M KH2PO4 and 0.1 M HEPES pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 6761 / % possible obs: 100 % / Redundancy: 36.5 % / Biso Wilson estimate: 80.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.132 / Net I/σ(I): 43.5
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 1.41 / Mean I/σ(I) obs: 3 / Num. unique obs: 658 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AK8

7ak8


Resolution: 2.75→29.68 Å / SU ML: 0.3331 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 33.6084
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.277 308 4.84 %
Rwork0.2487 6054 -
obs0.2501 6362 94.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.5 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 5 2 1484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961512
X-RAY DIFFRACTIONf_angle_d1.16212062
X-RAY DIFFRACTIONf_chiral_restr0.0636239
X-RAY DIFFRACTIONf_plane_restr0.0106268
X-RAY DIFFRACTIONf_dihedral_angle_d6.1705204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-3.470.35521510.27582829X-RAY DIFFRACTION91.52
3.47-29.680.25751570.2423225X-RAY DIFFRACTION97.77

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