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- PDB-9ro8: Pantoea ananatis encodes an antibacterial and anti-eukaryotic hum... -

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Basic information

Entry
Database: PDB / ID: 9ro8
TitlePantoea ananatis encodes an antibacterial and anti-eukaryotic human CD38 homologue T6SS ADP-ribosyl cyclase polymorphic toxin
ComponentsADP-ribosylcyclase toxin
KeywordsTOXIN / secreted toxin / ADP-ribosylcyclase / CD38 / ADP-ribosylhydrolase / type VI secretion system / polymorphic toxin
Function / homologyPAAR motif / PAAR motif / Uncharacterized protein
Function and homology information
Biological speciesPantoea ananatis LMG 20103 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsMartinkus, J. / Terradot, L. / Jurenas, D. / Cascales, E.
Funding support Belgium, France, 4items
OrganizationGrant numberCountry
Fonds National de la Recherche Scientifique (FNRS)FNRS-MIS F4526.23 Belgium
Walloon Excellence in Lifesciences & BIOtechnology (WELBIO)STG-X.251 Belgium
Agence Nationale de la Recherche (ANR)ANR-20-CE11-0017 France
Fondation pour la Recherche Medicale (FRM)DEQ20180339165 France
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Widespread deployment of the human CD38 ADP-ribosyl cyclase fold in antibacterial and anti-eukaryotic polymorphic toxins.
Authors: Martinkus, J. / Terradot, L. / Jurenas, D. / Cascales, E.
History
DepositionJun 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 12, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribosylcyclase toxin
B: ADP-ribosylcyclase toxin


Theoretical massNumber of molelcules
Total (without water)32,8472
Polymers32,8472
Non-polymers00
Water5,260292
1
A: ADP-ribosylcyclase toxin


Theoretical massNumber of molelcules
Total (without water)16,4231
Polymers16,4231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylcyclase toxin


Theoretical massNumber of molelcules
Total (without water)16,4231
Polymers16,4231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.230, 70.213, 96.119
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 252 through 254 or resid 256...
d_2ens_1(chain "B" and (resid 252 through 254 or resid 256...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERILEILEAA252 - 25414 - 16
d_12LEULEULYSLYSAA256 - 25718 - 19
d_13ILEILEGLNGLNAA259 - 34421 - 106
d_14ASNASNVALVALAA350 - 355112 - 117
d_15LEULEUARGARGAA357 - 385119 - 147
d_21SERSERILEILEBB252 - 25414 - 16
d_22LEULEULYSLYSBB256 - 25718 - 19
d_23ILEILEPROPROBB259 - 31021 - 72
d_24GLNGLNVALVALBB318 - 35580 - 117
d_25LEULEUARGARGBB357 - 385119 - 147

NCS oper: (Code: givenMatrix: (-0.441532539991, -0.78112838964, 0.441460592836), (-0.74614075239, 0.592917798299, 0.302857164491), (-0.49832017193, -0.195670445797, -0.844624225848)Vector: -13. ...NCS oper: (Code: given
Matrix: (-0.441532539991, -0.78112838964, 0.441460592836), (-0.74614075239, 0.592917798299, 0.302857164491), (-0.49832017193, -0.195670445797, -0.844624225848)
Vector: -13.1664526344, -13.2511633349, 41.9224208653)

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Components

#1: Protein ADP-ribosylcyclase toxin


Mass: 16423.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pantoea ananatis LMG 20103 (bacteria) / Gene: PANA_2924 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D4GKQ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 6000 (20 % w/v), pH 5.0, 0.1 M Sodium acetate, 0.2 M Ammonium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.82656 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 1.59→44.24 Å / Num. obs: 40681 / % possible obs: 99.5 % / Redundancy: 13.2 % / Biso Wilson estimate: 21.48 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.027 / Rrim(I) all: 0.096 / Net I/σ(I): 17
Reflection shellResolution: 1.59→1.63 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.053 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2765 / CC1/2: 0.758 / Rpim(I) all: 0.308 / Rrim(I) all: 1.099 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→39.66 Å / SU ML: 0.187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.6521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2157 2000 4.93 %
Rwork0.1831 38577 -
obs0.1847 40577 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.34 Å2
Refinement stepCycle: LAST / Resolution: 1.59→39.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 0 292 2282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00982052
X-RAY DIFFRACTIONf_angle_d1.03962784
X-RAY DIFFRACTIONf_chiral_restr0.076316
X-RAY DIFFRACTIONf_plane_restr0.008364
X-RAY DIFFRACTIONf_dihedral_angle_d14.0026770
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.24170760175 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.28861360.24312610X-RAY DIFFRACTION96.38
1.63-1.680.27381400.21792695X-RAY DIFFRACTION99.96
1.68-1.730.25041410.21492741X-RAY DIFFRACTION99.93
1.73-1.780.27061410.23322717X-RAY DIFFRACTION100
1.78-1.850.26291430.22212754X-RAY DIFFRACTION99.97
1.85-1.920.21051420.18772731X-RAY DIFFRACTION100
1.92-2.010.2071410.17222731X-RAY DIFFRACTION99.97
2.01-2.110.21941420.17072743X-RAY DIFFRACTION99.97
2.11-2.250.25851430.18492754X-RAY DIFFRACTION100
2.25-2.420.18891430.17472747X-RAY DIFFRACTION100
2.42-2.660.20151430.1782777X-RAY DIFFRACTION100
2.66-3.050.22681450.18492790X-RAY DIFFRACTION100
3.05-3.840.20111460.17642823X-RAY DIFFRACTION100
3.84-39.660.19871540.17472964X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.71671406604-0.726837863148-0.7006269183553.6372789369-0.1910863073872.55546069831-0.0726585075888-0.2051662391140.03227476721360.3121375149330.0976430302918-0.0308808285901-0.02544404816040.02486350059190.01843776768490.1805098933660.02247446404040.008648091495750.187995095140.01347707272280.13753315167-1.20858808425-8.5954227590647.3424025792
27.606312529425.72205668693-3.080297972484.80503515612-3.480180656824.536535368560.100234648056-0.1488625800490.610771506160.950265546013-0.115900848630.152271053756-0.6995001321740.416470140389-0.001517842817610.32375398037-0.0320492671471-0.08789545723420.2058579105020.008497114910220.27917063200214.3756001488-2.2272572275349.2441566169
37.080484281827.224309306713.064383320867.840375318493.796163722914.49268534837-0.232313523730.299371250388-0.042812238488-0.1948519255810.326069249143-0.416403646961-0.2997340725710.404163080674-0.1407529589170.1658005373640.0063317497487-0.02729440191030.1965961863360.01516839004570.20923956317314.0855768881-7.0876929018340.6843023323
43.55506749747-1.77872842243-1.74898466186.090230189990.5084521454714.028453911760.1390695623750.2253704357640.378418884384-0.2172958632650.15903309951-0.204501324623-0.3238690885960.135670167544-0.2622230082240.128507895676-0.0149821292073-0.009615414394020.2126077395310.00101664135990.147824031119-0.0770189893029-5.4664916934733.7468574078
53.153861724850.457804958684-0.3295045324912.04122294851-1.453427825933.84388940294-0.1622757145110.5629012813040.0690924508648-0.397998782142-0.0250985805564-0.656539085884-0.01931614205690.7370773244640.0990072455960.206269880196-0.00529777453465-0.01560260857850.3392925649470.06703495911040.258681851615.47981530159-10.861204716929.8295327159
64.84373734791-4.1281063206-3.022465155297.508768415133.689481164343.758211942280.09348523169040.03799474560330.112723774595-0.0412943752221-0.02126667240480.176636280817-0.10955316697-0.263183761565-0.05408239304970.148053895640.00513773777474-0.0155691251780.1834769848910.02528825086050.135420629078-8.16023378984-6.466775785835.2124057163
78.49946540329-2.49188201893-6.585987935876.457386973535.404564786717.798461619250.1497496815940.316698777519-0.209565272755-0.237700529314-0.169398791170.017709901581-0.0685714269655-0.2064843168680.03845879992710.2062489164070.0271307569522-0.03070849973290.2444926158610.01863674522090.150529261171-6.12304560545-10.617884212827.6413566878
82.585426743410.2708069688070.07740581877934.3052554056-0.4125111242893.66322905190.06138175859370.0184550062019-0.63870522287-0.3256903619040.0420049211860.2399458152760.616710806611-0.358372622483-0.1261796226940.212744375563-0.0485289299375-0.06862228408260.1789958285960.01137211014780.243106601275-10.2730627362-17.2998916449.23032144209
96.71347009839-3.112292342770.1260707912493.9328344367-0.9858755411756.21084413273-0.297251024736-0.2013606613150.443536065139-0.164978666360.2652424168940.687661708323-0.560205358243-0.326096479020.04611844534850.2279154747040.0466559303779-0.0721101487220.231670987887-0.004705626043160.316483812818-17.41880690625.310072313929.03158094011
101.89732437686-0.0717516741134-0.07232160869145.10739524696-1.54867771853.26679604375-0.0553432048790.0969787136832-0.094056847063-0.5578223343550.05268439709350.2742102566730.0816142606685-0.1281031604530.008382760737050.206679080618-0.0292952620933-0.05283135340090.1806108288080.006071007067940.190721781394-11.3078062041-7.682896290152.06874969619
112.82992029191-0.151154183388-1.816543230165.492343940420.2567943182434.174631579540.225514620866-0.324428164694-0.228849247291-0.419937377742-0.2458479504830.6237091342410.630022908202-0.661195236312-0.1869175875260.314019155219-0.100750911215-0.09520146701210.370233889982-0.02494078845480.351610700435-19.6972938819-19.42766831336.17168449061
127.856799212891.08940087996-1.104622903566.70871891312-1.320144308075.34542167955-0.0174057455638-0.227226669769-0.1930822358880.259912246818-0.06119972785660.735555339160.410638222485-0.8172368078450.0290878450690.160077864884-0.05172827306010.01255865126020.227120131665-0.02871517086760.206591798548-13.9331814626-16.185366306214.6076776189
132.35088535015-0.9214839091010.4084090013436.96965165974-1.062712328514.51641243648-0.0914815008942-0.1834388994050.04254414608040.462142648490.06826631620950.371734178026-0.356383674055-0.3962473857460.02592148968730.1366664930210.0117698496799-0.01191194529550.174739376687-0.02369639130610.130170098724-10.1543872307-3.7495005981215.4684969907
144.81532421795-0.925842806680.01234616501256.06582405546-1.158662113955.71153994783-0.102370418098-0.1680745057790.05964971816610.1609885689380.0715599097195-0.07776958923840.2092665692040.266193300434-0.04024734595090.2030315243660.00201067889834-0.004127168133150.2020035922780.006786623975820.148019925347-3.01166996531-11.830339657818.9963720202
152.40541745989-1.918300290241.594228505256.46553653835-2.338944592034.14246172703-0.1675459434460.001155243309240.18434053875-0.1848632022040.0508864065783-0.0643681202256-0.3813011095660.1031165640320.1525798659790.199980457807-0.0491192239513-0.0222876908960.183481142164-0.01621554052510.187572621657-4.062096229071.532019146929.99334912463
164.69927939812-2.544832996862.122619319099.02012468801-5.842015092255.044685833160.0401642478518-0.237310444596-0.120686950012-0.02420090379570.168892249582-0.1750173459550.233207657597-0.169721016365-0.1282168818350.239283044173-0.039965567367-0.05946679351120.328452768173-0.04468178058320.2758239541.83425067677-0.9698564393216.0906211713
178.016995969485.07970418825-0.3515505723528.36309266896-0.04150455562025.601032252560.1162430957010.33205631460.162986470968-0.1629574518540.00205344221317-0.800772780967-0.369417601930.757709333868-0.2526200941630.214353254882-0.0109223445508-0.002844696759120.2561539829090.01963715233010.2732040351318.5767843494-13.163879590145.0381297184
182.09678396616-1.14476715936-0.3023804912814.697467274130.9706448019382.79536786695-0.0549544832664-0.0391576361583-0.1306027875660.06494134126350.16966037507-0.05546788916710.1249678827-0.0392610915451-0.1199628458960.1499999060280.00202955805404-0.0057238242230.184933441060.002912700106120.1514282573340.154003291453-12.478450479839.932900488
191.241103447782.58232285448-0.4703342966397.659270551060.1094047685622.220268811320.0566016275334-0.2093548255650.365349703985-0.164545071177-0.1128012340680.104557088195-0.589938958227-0.462257033130.009406928358160.2641187356190.02443860730130.05009173440040.195902151424-0.02134151978340.247906598549-6.072556719295.3589329791841.8629117801
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 283 through 304 )BB283 - 30434 - 55
22chain 'B' and (resid 305 through 316 )BB305 - 31656 - 67
33chain 'B' and (resid 317 through 333 )BB317 - 33368 - 84
44chain 'B' and (resid 334 through 355 )BB334 - 35585 - 101
55chain 'B' and (resid 356 through 365 )BB356 - 365102 - 111
66chain 'B' and (resid 366 through 378 )BB366 - 378112 - 124
77chain 'B' and (resid 379 through 385 )BB379 - 385125 - 131
88chain 'A' and (resid 252 through 274 )AA252 - 2741 - 23
99chain 'A' and (resid 275 through 282 )AA275 - 28224 - 31
1010chain 'A' and (resid 283 through 304 )AA283 - 30432 - 53
1111chain 'A' and (resid 305 through 318 )AA305 - 31854 - 60
1212chain 'A' and (resid 319 through 333 )AA319 - 33361 - 75
1313chain 'A' and (resid 334 through 355 )AA334 - 35576 - 97
1414chain 'A' and (resid 356 through 365 )AA356 - 36598 - 107
1515chain 'A' and (resid 366 through 378 )AA366 - 378108 - 120
1616chain 'A' and (resid 379 through 385 )AA379 - 385121 - 127
1717chain 'B' and (resid 250 through 263 )BB250 - 2631 - 14
1818chain 'B' and (resid 264 through 274 )BB264 - 27415 - 25
1919chain 'B' and (resid 275 through 282 )BB275 - 28226 - 33

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