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- PDB-9g7p: Crystal structure of Shewanella putrefaciens PE-like toxin, Spx -

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Basic information

Entry
Database: PDB / ID: 9g7p
TitleCrystal structure of Shewanella putrefaciens PE-like toxin, Spx
ComponentsShewanella putrefaciens PE-like toxin catalytically inactive mutant
KeywordsTOXIN / Mono-ADP Ribosylating Toxin / exotoxin A / bacterial toxin
Biological speciesShewanella putrefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.861 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
AAA: Shewanella putrefaciens PE-like toxin catalytically inactive mutant
BBB: Shewanella putrefaciens PE-like toxin catalytically inactive mutant
CCC: Shewanella putrefaciens PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,11813
Polymers200,4683
Non-polymers65010
Water22,3571241
1
AAA: Shewanella putrefaciens PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0314
Polymers66,8231
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Shewanella putrefaciens PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0565
Polymers66,8231
Non-polymers2334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: Shewanella putrefaciens PE-like toxin catalytically inactive mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0314
Polymers66,8231
Non-polymers2083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.196, 121.196, 125.216
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Shewanella putrefaciens PE-like toxin catalytically inactive mutant


Mass: 66822.719 Da / Num. of mol.: 3 / Mutation: E556A
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.) Shewanella putrefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: NAD+-diphthamide ADP-ribosyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1241 / Source method: isolated from a natural source / Formula: H2O
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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000 (condition C10 of the PACT premier 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: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.79→104.83 Å / Num. obs: 193517 / % possible obs: 100 % / Redundancy: 21.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.062 / Rrim(I) all: 0.287 / Net I/σ(I): 7.5
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 21.2 % / Rmerge(I) obs: 3.695 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 9625 / CC1/2: 0.339 / Rpim(I) all: 0.811 / Rrim(I) all: 3.784 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.861→104.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.488 / SU ML: 0.122 / Cross valid method: FREE R-VALUE / ESU R: 0.135 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2204 8476 4.925 %
Rwork0.185 163640 -
all0.187 --
obs-172116 99.694 %
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: 34.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.486 Å20.243 Å2-0 Å2
2--0.486 Å2-0 Å2
3----1.576 Å2
Refinement stepCycle: LAST / Resolution: 1.861→104.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13905 0 40 1241 15186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01314292
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712918
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.63819539
X-RAY DIFFRACTIONr_angle_other_deg1.2211.5729712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73151803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93922.51777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.536152103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8381593
X-RAY DIFFRACTIONr_chiral_restr0.0530.21899
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216629
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023333
X-RAY DIFFRACTIONr_nbd_refined0.190.22648
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1790.211963
X-RAY DIFFRACTIONr_nbtor_refined0.1520.26934
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.26242
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.21030
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0790.26
X-RAY DIFFRACTIONr_metal_ion_refined0.2550.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2450.224
X-RAY DIFFRACTIONr_nbd_other0.1760.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.226
X-RAY DIFFRACTIONr_mcbond_it1.793.4667230
X-RAY DIFFRACTIONr_mcbond_other1.7893.4667229
X-RAY DIFFRACTIONr_mcangle_it2.8765.1899027
X-RAY DIFFRACTIONr_mcangle_other2.8765.1899028
X-RAY DIFFRACTIONr_scbond_it2.2473.7987062
X-RAY DIFFRACTIONr_scbond_other2.2463.7987063
X-RAY DIFFRACTIONr_scangle_it3.6865.58710512
X-RAY DIFFRACTIONr_scangle_other3.6865.58710513
X-RAY DIFFRACTIONr_lrange_it5.4941.67415869
X-RAY DIFFRACTIONr_lrange_other5.4441.43315632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.861-1.9090.3335680.33211835X-RAY DIFFRACTION96.6493
1.909-1.9610.3215660.30511784X-RAY DIFFRACTION99.2127
1.961-2.0180.2756170.27311473X-RAY DIFFRACTION100
2.018-2.080.275240.24811237X-RAY DIFFRACTION100
2.08-2.1480.2595020.22810882X-RAY DIFFRACTION100
2.148-2.2240.2585980.2110429X-RAY DIFFRACTION100
2.224-2.3080.2414880.19510141X-RAY DIFFRACTION100
2.308-2.4020.2164840.1889734X-RAY DIFFRACTION100
2.402-2.5090.254830.1849299X-RAY DIFFRACTION100
2.509-2.6310.2225020.1778920X-RAY DIFFRACTION100
2.631-2.7730.2394620.1778432X-RAY DIFFRACTION100
2.773-2.9410.2174460.1728008X-RAY DIFFRACTION100
2.941-3.1440.2273940.1817498X-RAY DIFFRACTION100
3.144-3.3960.2273900.1847024X-RAY DIFFRACTION100
3.396-3.720.2223100.1766452X-RAY DIFFRACTION100
3.72-4.1580.1832960.1555882X-RAY DIFFRACTION100
4.158-4.80.1643170.1335101X-RAY DIFFRACTION100
4.8-5.8760.1882720.1624255X-RAY DIFFRACTION100
5.876-8.2970.2041670.1733391X-RAY DIFFRACTION100
8.297-104.830.195900.1711863X-RAY DIFFRACTION100

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