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- PDB-9g7n: Crystal structure of Chromobacterium haemolyticum PE-like toxin, Hmx -

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Basic information

Entry
Database: PDB / ID: 9g7n
TitleCrystal structure of Chromobacterium haemolyticum PE-like toxin, Hmx
ComponentsExotoxin A
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
ACETATE ION / IMIDAZOLE / Exotoxin A
Similarity search - Component
Biological speciesChromobacterium haemolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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: Exotoxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6184
Polymers68,4211
Non-polymers1973
Water14,052780
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.325, 76.019, 130.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Exotoxin A


Mass: 68421.047 Da / Num. of mol.: 1 / Mutation: E572A
Source method: isolated from a genetically manipulated source
Details: Recombinant protein expressed with a cleavable poly-histidine tag with amino acid -1 to 0 residual after TEV cleavage
Source: (gene. exp.) Chromobacterium haemolyticum (bacteria)
Gene: B0T45_19615 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1W0CH45
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.12 M Monosaccharides, 0.1 M Buffer System 1 pH 6.5, 37.5 % v/v Precipitant Mix 4 (condition F4 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: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→65.69 Å / Num. obs: 143804 / % possible obs: 99.1 % / Redundancy: 11.8 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 16.3
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6411 / CC1/2: 0.437 / Rpim(I) all: 1.013 / Rrim(I) all: 1.856 / % possible all: 90.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→65.686 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.895 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.049 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.173 7165 4.993 %
Rwork0.1368 136336 -
all0.139 --
obs-143501 98.935 %
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: 23.398 Å2
Baniso -1Baniso -2Baniso -3
1--0.217 Å2-0 Å20 Å2
2--2.139 Å2-0 Å2
3----1.922 Å2
Refinement stepCycle: LAST / Resolution: 1.35→65.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4821 0 14 780 5615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135044
X-RAY DIFFRACTIONr_bond_other_d0.0040.0154712
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.6466878
X-RAY DIFFRACTIONr_angle_other_deg1.4351.57810859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895641
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.10721.575273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42315811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3911540
X-RAY DIFFRACTIONr_chiral_restr0.080.2656
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025834
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021198
X-RAY DIFFRACTIONr_nbd_refined0.2120.2968
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24278
X-RAY DIFFRACTIONr_nbtor_refined0.1660.22409
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2560
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1340.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0990.211
X-RAY DIFFRACTIONr_nbd_other0.1540.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1380.229
X-RAY DIFFRACTIONr_mcbond_it2.2582.1242509
X-RAY DIFFRACTIONr_mcbond_other2.2562.1222507
X-RAY DIFFRACTIONr_mcangle_it2.8783.2053140
X-RAY DIFFRACTIONr_mcangle_other2.8783.2073141
X-RAY DIFFRACTIONr_scbond_it2.9472.4962535
X-RAY DIFFRACTIONr_scbond_other2.9472.4962536
X-RAY DIFFRACTIONr_scangle_it3.6053.6123728
X-RAY DIFFRACTIONr_scangle_other3.6053.6133729
X-RAY DIFFRACTIONr_lrange_it4.55927.6555861
X-RAY DIFFRACTIONr_lrange_other4.21526.435620
X-RAY DIFFRACTIONr_rigid_bond_restr3.74439756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.35-1.3850.3124410.29892290.299106110.8480.87191.13180.295
1.385-1.4230.2944800.2795100.271103470.8880.88796.54970.263
1.423-1.4640.2524930.23295700.233101000.920.92399.63370.217
1.464-1.5090.2374790.19592720.19797640.9340.94699.86690.173
1.509-1.5590.2094750.16289780.16594790.9470.9699.72570.138
1.559-1.6130.2024720.14786960.1592120.9520.96699.52240.123
1.613-1.6740.1954470.13383730.13688600.9530.96899.54850.111
1.674-1.7430.1724530.11380940.11785730.9660.97799.69670.094
1.743-1.820.1864040.11477800.11882070.9530.97599.71970.098
1.82-1.9090.1664130.11374290.11678530.9660.97599.85990.099
1.909-2.0120.1623940.11270990.11575070.9680.98199.81350.101
2.012-2.1340.1683320.11667510.11970860.9690.97899.95770.105
2.134-2.2810.1573190.11363570.11566790.9740.97999.95510.104
2.281-2.4640.1553330.10659070.10962430.9730.98199.9520.099
2.464-2.6980.1522470.11354900.11557370.9730.9781000.107
2.698-3.0160.1832910.12549590.12852500.960.9731000.119
3.016-3.4820.1572660.13743660.13846320.970.9731000.134
3.482-4.2610.1431980.1337560.13139540.9780.9791000.129
4.261-6.0130.1721430.1529810.15131240.9770.981000.15
6.013-65.6860.184840.18617400.18618280.9670.96699.78120.182

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