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- PDB-9g7o: Crystal structure of Janthinobacterium lividum PE-like toxin, Jlx -

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Basic information

Entry
Database: PDB / ID: 9g7o
TitleCrystal structure of Janthinobacterium lividum PE-like toxin, Jlx
ComponentsJanthinobacterium lividum PE-like toxin catalytically inactive mutant
KeywordsTOXIN / Mono-ADP Ribosylating Toxin / exotoxin A / bacterial toxin
Function / homologyIMIDAZOLE / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesJanthinobacterium lividum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMasuyer, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Discovery of mono-ADP ribosylating toxins with high structural homology to Pseudomonas exotoxin A.
Authors: Masuyer, G. / Taverner, A. / MacKay, J. / Lima Marques, A.R. / Wang, Y. / Hunter, T. / Liu, K. / Mrsny, R.J.
History
DepositionJul 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 26, 2025Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
B: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
C: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
D: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,95324
Polymers270,9564
Non-polymers1,99720
Water28,3381573
1
A: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1256
Polymers67,7391
Non-polymers3865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4347
Polymers67,7391
Non-polymers6956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3386
Polymers67,7391
Non-polymers5995
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Janthinobacterium lividum PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0565
Polymers67,7391
Non-polymers3174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.625, 143.241, 110.670
Angle α, β, γ (deg.)90.000, 119.351, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Janthinobacterium lividum PE-like toxin catalytically inactive mutant


Mass: 67739.047 Da / Num. of mol.: 4 / Mutation: E571A
Source method: isolated from a genetically manipulated source
Details: Recombinant protein expressed with a cleavable poly-histidine tag with amino acid 0 residual after TEV cleavage
Source: (gene. exp.) Janthinobacterium lividum (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: NAD+-diphthamide ADP-ribosyltransferase

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Non-polymers , 6 types, 1593 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1573 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 57.05 %
Crystal growTemperature: 294.16 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Amino acids, 0.1 M Buffer System 1 pH 6.5, 30 % v/v Precipitant Mix 1 (condition H1 of the Morpheus Screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.75→115.6 Å / Num. obs: 186952 / % possible obs: 94.6 % / Redundancy: 14.1 % / CC1/2: 1 / Rpim(I) all: 0.028 / Rrim(I) all: 0.103 / Net I/σ(I): 12.5
Reflection shellResolution: 1.75→1.95 Å / Redundancy: 14.7 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 9348 / CC1/2: 0.722 / Rpim(I) all: 0.558 / Rrim(I) all: 2.15 / % possible all: 71.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→115.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.24 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.21 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2475 9406 5.031 %
Rwork0.2134 177544 -
all0.215 --
obs-186950 61.065 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 31.048 Å2
Baniso -1Baniso -2Baniso -3
1--0.079 Å2-0 Å20.025 Å2
2---0.467 Å2-0 Å2
3---0.317 Å2
Refinement stepCycle: LAST / Resolution: 1.75→115.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19000 0 128 1573 20701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01319627
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518319
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.64326705
X-RAY DIFFRACTIONr_angle_other_deg1.2291.57742153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.89152457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.55821.5891045
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85153059
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.58815154
X-RAY DIFFRACTIONr_chiral_restr0.0570.22563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024604
X-RAY DIFFRACTIONr_nbd_refined0.20.23776
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.217303
X-RAY DIFFRACTIONr_nbtor_refined0.1570.29351
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.28864
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.21400
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2520.232
X-RAY DIFFRACTIONr_nbd_other0.3360.2108
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.228
X-RAY DIFFRACTIONr_mcbond_it1.9733.1539837
X-RAY DIFFRACTIONr_mcbond_other1.9723.1539836
X-RAY DIFFRACTIONr_mcangle_it3.2234.72112291
X-RAY DIFFRACTIONr_mcangle_other3.2234.72112292
X-RAY DIFFRACTIONr_scbond_it2.1993.4159790
X-RAY DIFFRACTIONr_scbond_other2.1963.4139787
X-RAY DIFFRACTIONr_scangle_it3.6045.01714414
X-RAY DIFFRACTIONr_scangle_other3.6045.01414409
X-RAY DIFFRACTIONr_lrange_it5.43537.03721899
X-RAY DIFFRACTIONr_lrange_other5.39236.921572
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7950.393240.386538X-RAY DIFFRACTION2.4835
1.795-1.8440.3661000.3431630X-RAY DIFFRACTION7.8604
1.844-1.8980.3331660.3272980X-RAY DIFFRACTION14.692
1.898-1.9560.3252450.3234609X-RAY DIFFRACTION23.285
1.956-2.020.3483460.3286737X-RAY DIFFRACTION35.0991
2.02-2.0910.3485570.3249401X-RAY DIFFRACTION51.1506
2.091-2.170.3346110.29911037X-RAY DIFFRACTION61.9706
2.17-2.2590.3166600.28511899X-RAY DIFFRACTION69.032
2.259-2.3590.3196620.27212493X-RAY DIFFRACTION75.9395
2.359-2.4740.2947460.25713583X-RAY DIFFRACTION85.8744
2.474-2.6080.2767600.24814378X-RAY DIFFRACTION95.9376
2.608-2.7660.2597720.22914161X-RAY DIFFRACTION99.9465
2.766-2.9570.2486760.20213390X-RAY DIFFRACTION99.9432
2.957-3.1940.2486090.20112468X-RAY DIFFRACTION99.9694
3.194-3.4980.2355810.19911478X-RAY DIFFRACTION99.9006
3.498-3.9110.2045430.18510397X-RAY DIFFRACTION99.9726
3.911-4.5150.1914710.169147X-RAY DIFFRACTION99.9584
4.515-5.5280.2074210.1627774X-RAY DIFFRACTION99.9878
5.528-7.8090.2142990.1866054X-RAY DIFFRACTION100
7.809-115.60.2231570.2033390X-RAY DIFFRACTION100

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