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- PDB-7uav: Structure of Clostridium botulinum prophage Tad1 in apo state -

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Basic information

Entry
Database: PDB / ID: 7uav
TitleStructure of Clostridium botulinum prophage Tad1 in apo state
ComponentsABC transporter ATPase
KeywordsVIRAL PROTEIN / Anti-Thoeris / Immune Evasion / signal sequestration
Function / homologyABC transporter ATPase
Function and homology information
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLu, A. / Leavitt, A. / Yirmiya, E. / Amitai, G. / Garb, J. / Morehouse, B.R. / Hobbs, S.J. / Sorek, R. / Kranzusch, P.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2022
Title: Viruses inhibit TIR gcADPR signalling to overcome bacterial defence.
Authors: Leavitt, A. / Yirmiya, E. / Amitai, G. / Lu, A. / Garb, J. / Herbst, E. / Morehouse, B.R. / Hobbs, S.J. / Antine, S.P. / Sun, Z.J. / Kranzusch, P.J. / Sorek, R.
History
DepositionMar 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 16, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter ATPase
B: ABC transporter ATPase
C: ABC transporter ATPase
D: ABC transporter ATPase
E: ABC transporter ATPase


Theoretical massNumber of molelcules
Total (without water)72,5935
Polymers72,5935
Non-polymers00
Water2,054114
1
A: ABC transporter ATPase
B: ABC transporter ATPase


Theoretical massNumber of molelcules
Total (without water)29,0372
Polymers29,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-34 kcal/mol
Surface area12680 Å2
MethodPISA
2
C: ABC transporter ATPase
D: ABC transporter ATPase


Theoretical massNumber of molelcules
Total (without water)29,0372
Polymers29,0372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-35 kcal/mol
Surface area12590 Å2
MethodPISA
3
E: ABC transporter ATPase

E: ABC transporter ATPase


Theoretical massNumber of molelcules
Total (without water)29,0372
Polymers29,0372
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area6620 Å2
ΔGint-33 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.954, 155.954, 161.448
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11C-228-

HOH

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Components

#1: Protein
ABC transporter ATPase / Tad1


Mass: 14518.660 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: FDB51_07880 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A846JTD7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris-HCl pH 7.5 and 40% PEG 200

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.2→48.67 Å / Num. obs: 38341 / % possible obs: 100 % / Redundancy: 41.5 % / Biso Wilson estimate: 50.31 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Net I/σ(I): 15.2
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 3296 / CC1/2: 0.705 / Rpim(I) all: 0.793

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→48.67 Å / SU ML: 0.2863 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2478 1999 5.22 %
Rwork0.2009 36303 -
obs0.2033 38302 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.26 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4696 0 0 114 4810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224761
X-RAY DIFFRACTIONf_angle_d0.39986369
X-RAY DIFFRACTIONf_chiral_restr0.0394668
X-RAY DIFFRACTIONf_plane_restr0.0033845
X-RAY DIFFRACTIONf_dihedral_angle_d13.8191866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29281390.29532524X-RAY DIFFRACTION99.07
2.26-2.320.34731410.28652561X-RAY DIFFRACTION99.89
2.32-2.380.28921430.26052597X-RAY DIFFRACTION99.93
2.38-2.460.29141400.25782566X-RAY DIFFRACTION99.96
2.46-2.550.29621430.25452581X-RAY DIFFRACTION99.96
2.55-2.650.27361420.24272580X-RAY DIFFRACTION99.96
2.65-2.770.27771410.23922570X-RAY DIFFRACTION99.96
2.77-2.920.25441430.2292586X-RAY DIFFRACTION100
2.92-3.10.31111430.23942587X-RAY DIFFRACTION99.93
3.1-3.340.25881420.22332598X-RAY DIFFRACTION100
3.34-3.680.26451440.19572598X-RAY DIFFRACTION99.93
3.68-4.210.2511440.17872617X-RAY DIFFRACTION100
4.21-5.30.18481440.15962619X-RAY DIFFRACTION100
5.3-48.670.22961500.1812719X-RAY DIFFRACTION99.93
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.3075974780.0407749683798-0.9453670585665.567265666530.009757421111622.84144504560.08918887766450.557177128571-0.955288623746-1.121732677310.2288877579120.3083551539961.17722208743-0.180496334834-0.1842570700190.6786447879070.00332673544247-0.07367381642440.507216706685-0.1914020238850.67362597709928.5048219204100.52733698934.4215961808
23.942435136992.359606233680.1273201578816.40071683217-2.789139050462.6197276467-0.01167132225950.789115108245-0.231027204542-0.9608489547260.0158935357567-0.1727680137130.4432172915540.3711771823220.01945982998740.5511523889380.03903379882950.02279691849330.55550402818-0.05537386181240.31999521585826.2670428322113.68565803128.7576287356
35.67740007747-1.351151983773.561233193545.876074415720.608475923448.583291879070.3077805938921.06107995978-4.47201554755-2.772227219410.6570418708091.225366321831.82625061606-1.59025855228-0.604000356841.44906114024-0.119870679584-0.3598130397451.02810822668-0.2216701345021.365628862812.369114340299.476810376427.2012455295
45.65507835372-0.2953889696561.169975131073.69963739921.741654768564.2343779934-0.4844154148781.130626395890.295980679333-0.6120792421161.068442938721.747826370270.257348523323-0.0729197568226-0.2398087088630.397064808568-0.04569258986570.001265094031550.522566139370.04399402446260.39364026274820.5633208412119.28582951431.6639739063
57.312767433242.134646447250.9414066923992.443013077442.306590867556.732656095150.009956184730130.5503423021360.8817846768880.157025393859-0.1626259639381.15712743343-1.589490702580.134304766960.004907058515180.5959245899040.0520764546078-0.02170411702250.3757639975160.007403978348390.42569229287420.971649507130.64103576732.3977360086
68.48537249079-0.9939006017490.9656440665711.083737221041.666336879562.65767467982-0.115693421484-0.44131362054-0.5032623125910.231748725225-0.0007125923509480.02519761988070.22921253025-0.1229051784980.07506455624570.4690027746650.002363151925570.01011907756990.4049627868780.0188172009040.35843887549824.5437292175109.70544401451.71257387
75.92023241319-1.12600288910.4380130780087.84956694092-0.6639644866313.90110247854-0.1004484625670.1892362768030.7084131893910.105877857754-0.1239751205960.00400801377372-0.5509070219810.06692379891960.1467725518540.5513935471940.0408113037757-0.06209131897080.5722209818328.32773697318E-60.49753302204433.6746110111130.04919347547.4455836247
83.258200891691.784211130330.5189336689171.718586811230.2235115976160.199798488627-0.331564726607-0.1100961847590.3837506632620.9047081328220.3224694216030.71693284118-0.355140109042-0.3077048395840.1396407550230.695905190950.107415429942-0.03476815717730.635777437414-0.001396534594760.56691883342319.602633779125.56398393250.0873431948
94.360531220550.1211325649161.037749496057.7926150072-1.509647793058.477235035730.0960360417877-0.1131279008910.04330988561930.933317754748-0.03242896030930.857416010762-0.809353952029-0.572076636337-0.0577060525410.2511600634710.05019183712850.08471222900880.536662150386-0.07323701988550.31268986093811.3849495965120.57487209643.4116454856
102.234442336460.207226675343-1.943396540397.923340299312.693850092892.652451936560.1651244337920.190316690482-0.665341697201-1.08022245289-0.3324705035941.760864103060.462967307895-0.6575840578180.2024880863130.63864915893-0.0852378660902-0.1371990449130.6107166313810.03588232070520.61835477613411.2984560546104.45116335239.3434672854
112.054354284190.118336660711.60036023790.9884477060070.5926305859674.29300718541-0.04845239765390.0953350800698-0.111183463133-0.05719556270970.108459699703-0.1987633954210.2101846370010.40139797563-0.1041119649170.3966511495690.06845219597670.009550004460810.353927925642-0.03168275771740.35017234893331.6177252241113.53399145239.7465218086
125.208485318520.7214200276860.4429298919068.357272214253.822527166714.247075137020.404076559001-0.260449119995-1.324778376570.7591466508430.09438051197890.9997256729550.852521885162-0.15726861905-0.5388153539790.7333065746840.0425771433764-0.09887540822140.5390621308150.08834441076290.85002753620829.040351852896.640335940846.9777227278
132.67137614762-1.25437852461-0.7929205901592.71097970655-2.875821016395.634293735990.4946559894020.3276242381870.977520275469-0.1882182934780.0197489971785-0.72183191682-1.246017072310.39322232311-0.628094316020.682663800965-0.1177245797320.007057903090070.494644925922-0.1555075314591.001634606216.5135826568107.95864609979.7159047591
143.9720216673-1.18359097432-2.50944751933.04109096593-1.207630116074.36639127790.541806366095-1.081638709311.305383402420.9743826291450.2605560611160.0785893878942-0.2198675843550.912716054485-0.8787696554990.904608816734-0.0877292496770.1100556032740.739077391662-0.3092541410031.036603013946.16579793032116.4477356587.925838971
155.060362236120.7457874016791.138545101542.102748227952.406446703462.757467342011.30939554789-0.6131912446761.482085092530.383018171435-0.8314037078761.31035234907-1.601942507351.60525798246-0.6382162586411.23983274476-0.2994064005330.3337377238420.925866491568-0.284501069451.1846555403917.9647513693125.95981697974.7530753719
168.109780590351.22503849961-2.300752118811.81411903234-0.1079352322372.00954828070.116312282923-0.05694988401671.204193542230.4863303805860.0845787017052-0.3176495105490.0545184094492-0.0189558091352-0.2985954313630.796231400008-0.0354900611790.201185085890.528290209962-0.1331166585531.0515618861-0.458704836765120.32172579584.1629637762
173.585018760523.37489474221.73132414993.244463612651.988588079982.093369647220.253533570066-1.353559980061.182456518260.7264506993730.0001933684629830.000760117097298-1.15339012344-1.105513038320.1226060606340.9194506683250.128906878110.2510792189020.985962677467-0.06430593166081.14433723484-10.8371908006121.66164684987.7921347374
182.482792118030.377663248334-0.009453177351713.696613340210.1934459525095.880550833120.2238530159290.3662538163360.707621387994-0.02258187350230.02868187178420.659215794579-0.831527893136-1.3471145968-0.3065787845020.5426667886510.04565131653880.09459729585960.4188732083580.04074164249420.697398368226-1.41813105992107.41132845670.1716996957
193.709688528091.2044836438-1.822327254734.38873486029-2.198068497465.51116271280.184377353667-0.3160884161030.449501679093-0.2199960507330.2046956963940.3132996604210.07181801162040.039868787484-0.2133993855150.495372982354-0.02801808508250.04738488117910.424264395806-0.002407554584340.537939860862-0.45728330200799.227165356571.8518681836
205.97398151957-0.0489161003275-1.694582891975.47810906816-0.7107232930674.129400236910.471262062245-2.11315145321-0.8109800203731.5432717355-0.1442658816271.2914691419-0.302977980669-0.248776392015-0.5257280393960.906522686025-0.03463213773640.3510426008490.990975079397-0.044644861441.16419630526-17.0305557989102.69797770487.7208877115
213.1242375809-1.196145104750.2462221261186.842035598332.562023941921.115713960660.7120083285110.6299976856221.0742376719-0.914393878206-0.007728934994240.707721599031-0.822420417007-0.612576452898-0.5422313417140.7728941342430.1574234455140.1589727836430.5256634244850.1678278746860.905088822173-7.14403368814114.0331631769.4781779759
229.158976735620.9732369059950.584144412041.214610893430.006352593019910.3500788759430.0846919102167-0.3603418040522.01156846905-0.633443613627-0.7141993942310.503254679247-1.96256054455-0.9526214663660.4052241295691.209142006560.165600846827-0.03130976120080.750033899923-0.03446934957021.55847012124-14.8075026111127.30393951276.8857246797
231.733917097660.5597680183650.4542510275434.17512953419-0.9357420400681.794817969670.262620502062-0.2468795000910.5847608991030.1490970070170.0970382253415-0.122696087919-0.3450197255640.191321262429-0.3550726680040.604058621504-0.009070822286750.1345869836330.445821408489-0.1054464260460.6901423284124.88276146719108.5432380278.5613596175
246.591108658544.47111911046-4.117279425682.9796535386-2.671661978052.728884189320.2881609699591.78811357653-0.602695916781-1.51831360942-0.441745642492-0.570908559947-0.442312204849-0.6564549477850.2168713766171.05223075408-0.01362992278220.1346931469930.822449515924-0.08675313036541.1422498547419.1391001441100.58222799568.0807806204
255.12509788961-2.15811132542-2.102657701862.07186130928-0.4425089808992.6663280043-0.3739228071-0.396740782591-0.2605970655441.29227058318-0.11490981577-1.948689253570.3196796907981.447122214020.5527382153650.7239496111110.156033001848-0.2295217671680.759848078025-0.09790334363641.1158684245961.1595031403100.24439004761.8578897222
264.011660264580.6781568053062.792964906482.963732522910.4473289743593.881287320950.1775680856561.41188814721-2.02081419755-0.8701135163350.575832300966-1.217897478020.7937829173522.036817993770.1746515226910.449055313590.4157664245430.02381715791350.823078331588-0.1851956953381.4499383649862.552653664293.02057939149.2199949438
273.27502477414-4.529053871794.010167614766.49700544945-5.682838976375.099783040370.563524407901-0.4425298121060.463519143936-0.0113991558111-0.354108716959-0.73467099767-0.4067062876021.45159092120.1962790965111.034618188810.263037661591-0.1894205306971.122175377870.09290880460481.6499257206467.409748735584.178568841966.3885521387
284.37335950862.63942986381.266630959421.873807593371.018835340752.86715411887-0.1656025725860.453768666615-0.6946865387320.3724661553580.873057986337-1.069294311991.337613314510.391963408316-0.9068169530650.8048136960630.3789814983430.02912515279720.668467422511-0.1474861663021.4005611496955.998220326884.658508456641.9503429147
293.256941928130.575927530132-0.1172518124164.363346311271.113344799575.54832395125-0.009746800321230.0507563813006-0.8091518286220.0605828806115-0.00488667543322-0.1025701718470.5017823843920.08151009032440.1852260819320.466466807170.104002269206-0.02799656048740.3072201812120.008422940985570.71842340880743.06974689695.318577427355.5538845858
302.3267891941-3.26599222685-3.259411358056.660133508136.169328358886.11721743590.8241343148430.8669150871290.0613481662107-1.59046321185-0.6405764569010.20392671339-0.6819714578061.361884316340.2511423552111.070515245490.2512893703260.04524834900471.00967008132-0.2320517993140.80348057581741.211605359197.789173810334.359516005
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 13 )AA2 - 131 - 12
22chain 'A' and (resid 14 through 35 )AA14 - 3513 - 34
33chain 'A' and (resid 36 through 46 )AA36 - 4635 - 45
44chain 'A' and (resid 47 through 56 )AA47 - 5646 - 55
55chain 'A' and (resid 57 through 67 )AA57 - 6756 - 66
66chain 'A' and (resid 68 through 102 )AA68 - 10267 - 101
77chain 'A' and (resid 103 through 119 )AA103 - 119102 - 118
88chain 'B' and (resid 1 through 13 )BB1 - 131 - 13
99chain 'B' and (resid 14 through 46 )BB14 - 4614 - 46
1010chain 'B' and (resid 47 through 61 )BB47 - 6147 - 61
1111chain 'B' and (resid 62 through 102 )BB62 - 10262 - 102
1212chain 'B' and (resid 103 through 116 )BB103 - 116103 - 116
1313chain 'C' and (resid 3 through 13 )CC3 - 131 - 11
1414chain 'C' and (resid 14 through 35 )CC14 - 3512 - 33
1515chain 'C' and (resid 36 through 46 )CC36 - 4634 - 44
1616chain 'C' and (resid 47 through 56 )CC47 - 5645 - 54
1717chain 'C' and (resid 57 through 67 )CC57 - 6755 - 65
1818chain 'C' and (resid 68 through 84 )CC68 - 8466 - 82
1919chain 'C' and (resid 85 through 107 )CC85 - 10783 - 105
2020chain 'C' and (resid 108 through 117 )CC108 - 117106 - 115
2121chain 'D' and (resid 2 through 35 )DD2 - 351 - 34
2222chain 'D' and (resid 36 through 46 )DD36 - 4635 - 45
2323chain 'D' and (resid 47 through 107 )DD47 - 10746 - 106
2424chain 'D' and (resid 108 through 117 )DD108 - 117107 - 116
2525chain 'E' and (resid 2 through 13 )EE2 - 131 - 12
2626chain 'E' and (resid 14 through 35 )EE14 - 3513 - 34
2727chain 'E' and (resid 36 through 46 )EE36 - 4635 - 45
2828chain 'E' and (resid 47 through 61 )EE47 - 6146 - 60
2929chain 'E' and (resid 62 through 107 )EE62 - 10761 - 106
3030chain 'E' and (resid 108 through 117 )EE108 - 117107 - 116

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