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- PDB-9g7m: Crystal structure of Collimonas fungivorans PE-like toxin, Cfx -

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Basic information

Entry
Database: PDB / ID: 9g7m
TitleCrystal structure of Collimonas fungivorans PE-like toxin, Cfx
ComponentsExotoxin A-like protein
KeywordsTOXIN / Mono-ADP Ribosylating Toxin / exotoxin A / bacterial toxin
Function / homology
Function and homology information


NAD+-diphthamide ADP-ribosyltransferase activity
Similarity search - Function
Exotoxin A catalytic domain / Exotoxin A, binding / Exotoxin A, middle domain / Exotoxin A, middle domain superfamily / Exotoxin A catalytic / Exotoxin A binding / Exotoxin A, targeting / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Exotoxin A-like protein
Similarity search - Component
Biological speciesCollimonas fungivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Exotoxin A-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2292
Polymers68,1891
Non-polymers401
Water63135
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-9 kcal/mol
Surface area25520 Å2
Unit cell
Length a, b, c (Å)141.797, 141.797, 202.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Exotoxin A-like protein


Mass: 68188.711 Da / Num. of mol.: 1 / Mutation: E565A
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.) Collimonas fungivorans (bacteria) / Gene: BCF11_5153 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2A9JQY3
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 4.31 Å3/Da / Density % sol: 71.48 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium chloride hexahydrate 0.1 M BIS-Tris pH 5.5, 25 % w/v PEG 3350 (condition H11 of the JCSG-plus Screen, Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→70.9 Å / Num. obs: 30359 / % possible obs: 100 % / Redundancy: 39.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.493 / Rpim(I) all: 0.109 / Rrim(I) all: 0.5 / Net I/σ(I): 7.6
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 41.2 % / Rmerge(I) obs: 5.74 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4335 / CC1/2: 0.439 / Rpim(I) all: 1.257 / Rrim(I) all: 5.87 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→70.9 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.929 / SU B: 39.462 / SU ML: 0.326 / Cross valid method: FREE R-VALUE / ESU R: 0.452 / ESU R Free: 0.292
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2531 1483 4.894 %
Rwork0.2291 28819 -
all0.23 --
obs-30302 99.951 %
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: 83.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.519 Å20.259 Å2-0 Å2
2--0.519 Å2-0 Å2
3----1.683 Å2
Refinement stepCycle: LAST / Resolution: 2.8→70.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 1 35 4735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0124817
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164518
X-RAY DIFFRACTIONr_angle_refined_deg0.8981.6466569
X-RAY DIFFRACTIONr_angle_other_deg0.3021.56810362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385607
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.685538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25210738
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.88110223
X-RAY DIFFRACTIONr_chiral_restr0.0410.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021152
X-RAY DIFFRACTIONr_nbd_refined0.210.21033
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24230
X-RAY DIFFRACTIONr_nbtor_refined0.1740.22382
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2110
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4370.22
X-RAY DIFFRACTIONr_nbd_other0.1530.239
X-RAY DIFFRACTIONr_mcbond_it2.895.8982437
X-RAY DIFFRACTIONr_mcbond_other2.8875.8992437
X-RAY DIFFRACTIONr_mcangle_it4.99910.5983041
X-RAY DIFFRACTIONr_mcangle_other4.99910.63042
X-RAY DIFFRACTIONr_scbond_it2.5916.1762380
X-RAY DIFFRACTIONr_scbond_other2.5916.1742379
X-RAY DIFFRACTIONr_scangle_it4.60911.2033528
X-RAY DIFFRACTIONr_scangle_other4.60811.2043529
X-RAY DIFFRACTIONr_lrange_it7.93654.2195330
X-RAY DIFFRACTIONr_lrange_other7.93654.2315330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.3911200.3872065X-RAY DIFFRACTION99.9085
2.873-2.9510.3861160.3682024X-RAY DIFFRACTION100
2.951-3.0370.3711020.3521970X-RAY DIFFRACTION99.8554
3.037-3.130.328920.3241922X-RAY DIFFRACTION99.9008
3.13-3.2320.286740.2881902X-RAY DIFFRACTION100
3.232-3.3460.2891060.2841788X-RAY DIFFRACTION100
3.346-3.4720.359770.2871764X-RAY DIFFRACTION100
3.472-3.6130.274920.2451675X-RAY DIFFRACTION99.9434
3.613-3.7730.263760.2411632X-RAY DIFFRACTION100
3.773-3.9570.264730.2231567X-RAY DIFFRACTION100
3.957-4.170.198810.1851486X-RAY DIFFRACTION100
4.17-4.4220.255680.1761418X-RAY DIFFRACTION100
4.422-4.7260.167790.1611318X-RAY DIFFRACTION99.9285
4.726-5.1030.223590.161244X-RAY DIFFRACTION100
5.103-5.5870.227780.1881140X-RAY DIFFRACTION99.918
5.587-6.2420.272520.2191061X-RAY DIFFRACTION100
6.242-7.1980.271410.218949X-RAY DIFFRACTION100
7.198-8.7930.211470.172819X-RAY DIFFRACTION100
8.793-12.3410.201290.171657X-RAY DIFFRACTION100
12.341-70.90.178210.342418X-RAY DIFFRACTION99.5465
Refinement TLS params.Method: refined / Origin x: -36.5608 Å / Origin y: 8.7976 Å / Origin z: 18.3301 Å
111213212223313233
T0.0954 Å20.0023 Å2-0.0185 Å2-0.6979 Å20.0283 Å2--0.0372 Å2
L0.4666 °20.122 °2-0.2919 °2-0.306 °2-0.014 °2--0.3397 °2
S0.057 Å °0.0022 Å °-0.038 Å °-0.0325 Å °-0.0859 Å °-0.0913 Å °-0.0881 Å °-0.2928 Å °0.0289 Å °
Refinement TLS groupSelection: ALL

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