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- PDB-8za7: ART-ARH type toxin effector-immunity protein pair of Listeria mon... -

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Basic information

Entry
Database: PDB / ID: 8za7
TitleART-ARH type toxin effector-immunity protein pair of Listeria monocytogenes
Components
  • Lmo0066 protein
  • Lmo0067 protein
KeywordsTOXIN / toxin effector / immunity protein
Function / homology
Function and homology information


hydrolase activity / extracellular region / metal ion binding / membrane
Similarity search - Function
ADP-ribosylation/Crystallin J1 / ADP-ribosylglycohydrolase / ADP-ribosylation/Crystallin J1 superfamily / : / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile.
Similarity search - Domain/homology
Chem-AR6 / Lmo0067 protein / Lmo0066 protein
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsOuyang, S. / Hongxin, G. / Huan, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31271265 China
CitationJournal: To Be Published
Title: ART-ARH type toxin effector-immunity protein pair of Listeria monocytogenes
Authors: Ouyang, S. / Hongxin, G. / Huan, W.
History
DepositionApr 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmo0067 protein
B: Lmo0066 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7605
Polymers58,1522
Non-polymers6083
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.020, 84.020, 82.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Lmo0067 protein / Eri1 / Esx secretion ADP-ribosyl hydrolase immunity 1


Mass: 37890.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo0067 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YAQ0
#2: Protein Lmo0066 protein / Ere1 / Esx secretion ADP-ribosyltransferase effector 1


Mass: 20260.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: lmo0066 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YAQ1
#3: Chemical ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.9 Å3/Da / Density % sol: 57.62 %
Crystal growTemperature: 289.15 K / Method: counter-diffusion
Details: 0.2M Magnesium chloride, 0.1M Sodium cacolylate pH 6.5, 20% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→41.4 Å / Num. obs: 78696 / % possible obs: 100 % / Redundancy: 2.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.104 / Net I/σ(I): 9.2
Reflection shellResolution: 1.65→1.69 Å / Num. unique obs: 5848 / CC1/2: 0.651

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.49 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 3752 4.77 %
Rwork0.1677 --
obs0.1689 78646 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 38 556 4679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114207
X-RAY DIFFRACTIONf_angle_d1.2445691
X-RAY DIFFRACTIONf_dihedral_angle_d10.258570
X-RAY DIFFRACTIONf_chiral_restr0.062627
X-RAY DIFFRACTIONf_plane_restr0.012726
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.31251760.27372770X-RAY DIFFRACTION100
1.67-1.690.29811160.27062781X-RAY DIFFRACTION100
1.69-1.720.25331440.26062775X-RAY DIFFRACTION100
1.72-1.740.28661300.24482737X-RAY DIFFRACTION100
1.74-1.770.2656980.24762851X-RAY DIFFRACTION100
1.77-1.790.25081700.23152743X-RAY DIFFRACTION100
1.79-1.820.25881380.22672759X-RAY DIFFRACTION100
1.82-1.860.22221660.22222713X-RAY DIFFRACTION100
1.86-1.890.26591540.21962730X-RAY DIFFRACTION100
1.89-1.930.22481420.21162827X-RAY DIFFRACTION100
1.93-1.960.2811500.20242792X-RAY DIFFRACTION100
1.96-2.010.21861490.19612741X-RAY DIFFRACTION100
2.01-2.050.2291760.18322717X-RAY DIFFRACTION100
2.05-2.110.22821640.17592786X-RAY DIFFRACTION100
2.11-2.160.19411120.16622784X-RAY DIFFRACTION100
2.16-2.230.20961340.17342804X-RAY DIFFRACTION100
2.23-2.30.21311320.17142733X-RAY DIFFRACTION100
2.3-2.380.19921540.16012765X-RAY DIFFRACTION100
2.38-2.470.17241280.15492818X-RAY DIFFRACTION100
2.48-2.590.1781960.16092778X-RAY DIFFRACTION100
2.59-2.720.17781540.16452781X-RAY DIFFRACTION100
2.72-2.890.19261260.1672803X-RAY DIFFRACTION100
2.89-3.120.15691520.15522762X-RAY DIFFRACTION100
3.12-3.430.1831340.15622749X-RAY DIFFRACTION100
3.43-3.930.1722920.1432841X-RAY DIFFRACTION100
3.93-4.940.14651340.12762791X-RAY DIFFRACTION100
4.94-29.490.17751310.16472763X-RAY DIFFRACTION100

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