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- PDB-9ilr: The structure of the GmvT-GmvA-AcCoA ternary complex -

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Basic information

Entry
Database: PDB / ID: 9ilr
TitleThe structure of the GmvT-GmvA-AcCoA ternary complex
Components
  • DUF1778 domain-containing protein
  • N-acetyltransferase
KeywordsTOXIN / Toxin-antitoxin system / GNAT-RHH / acetylation / AcCoA / GmvAT
Function / homologyACETYL COENZYME *A / PHOSPHATE ION / :
Function and homology information
Biological speciesShigella sonnei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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)24,7494
Polymers23,8442
Non-polymers9052
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-27 kcal/mol
Surface area10070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.220, 67.220, 185.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 4.38 Å3/Da / Density % sol: 71.94 %
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: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→37.65 Å / Num. obs: 21054 / % possible obs: 99.9 % / Redundancy: 24.6 % / Biso Wilson estimate: 53.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.166 / Net I/σ(I): 15.7
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 22 % / Rmerge(I) obs: 2 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1532 / CC1/2: 0.767 / % possible all: 99.9

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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: 2.25→33.15 Å / SU ML: 0.2379 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.6805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2269 1021 4.87 %
Rwork0.2082 19948 -
obs0.209 20969 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.62 Å2
Refinement stepCycle: LAST / Resolution: 2.25→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 56 45 1654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00921654
X-RAY DIFFRACTIONf_angle_d1.2882256
X-RAY DIFFRACTIONf_chiral_restr0.0581253
X-RAY DIFFRACTIONf_plane_restr0.0152285
X-RAY DIFFRACTIONf_dihedral_angle_d10.5888225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.29081480.2832774X-RAY DIFFRACTION99.9
2.37-2.520.27881590.26972763X-RAY DIFFRACTION99.8
2.52-2.710.32511400.26512804X-RAY DIFFRACTION99.83
2.71-2.980.27921380.24282816X-RAY DIFFRACTION99.9
2.98-3.410.26231490.23072846X-RAY DIFFRACTION100
3.42-4.30.20141440.18612877X-RAY DIFFRACTION100
4.3-33.150.18941430.18523068X-RAY DIFFRACTION99.6

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