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- PDB-7skk: pertussis toxin in complex with ADPR and Nicotinamide -

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Basic information

Entry
Database: PDB / ID: 7skk
Titlepertussis toxin in complex with ADPR and Nicotinamide
ComponentsPertussis toxin subunit 1
KeywordsTOXIN / TRANSFERASE/INHIBITOR / ADP-RIBOSYLTRANSFERASE / TRANSFERASE / WHOOPING COUGH / INHIBITOR / PERTUSSIS / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / extracellular region
Similarity search - Function
Bordetella pertussis toxin A / Pertussis toxin, subunit 1
Similarity search - Domain/homology
Chem-AR6 / NICOTINAMIDE / Pertussis toxin subunit 1
Similarity search - Component
Biological speciesBordetella pertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65000771809 Å
AuthorsLittler, D.R. / Beddoe, T. / Pulliainen, A. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of pertussis toxin with NAD + and analogs provide structural insights into the mechanism of its cytosolic ADP-ribosylation activity.
Authors: Sakari, M. / Tran, M.T. / Rossjohn, J. / Pulliainen, A.T. / Beddoe, T. / Littler, D.R.
History
DepositionOct 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 18, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pertussis toxin subunit 1
B: Pertussis toxin subunit 1
C: Pertussis toxin subunit 1
D: Pertussis toxin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,10717
Polymers82,9014
Non-polymers3,20613
Water13,277737
1
A: Pertussis toxin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4073
Polymers20,7251
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pertussis toxin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5034
Polymers20,7251
Non-polymers7783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Pertussis toxin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5995
Polymers20,7251
Non-polymers8744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Pertussis toxin subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5995
Polymers20,7251
Non-polymers8744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.540, 68.140, 71.730
Angle α, β, γ (deg.)91.100, 90.200, 91.280
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Pertussis toxin subunit 1 / PTX S1 / Islet-activating protein S1 / IAP S1 / NAD-dependent ADP-ribosyltransferase


Mass: 20725.354 Da / Num. of mol.: 4 / Mutation: C41S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxA, BP3783 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P04977, Transferases; Glycosyltransferases; Pentosyltransferases, NAD+ ADP-ribosyltransferase
#2: Chemical
ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical
ChemComp-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.5M (NH4)2SO4 and 0.1M HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2014
RadiationMonochromator: Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→32 Å / Num. obs: 69920 / % possible obs: 88.9 % / Redundancy: 3.9 % / Biso Wilson estimate: 6.334 Å2 / CC1/2: 0.979 / Rpim(I) all: 0.071 / Net I/σ(I): 8.9
Reflection shellResolution: 1.65→1.74 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 6053 / CC1/2: 0.961 / Rpim(I) all: 0.1 / % possible all: 52.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRT

1prt


Resolution: 1.65000771809→31.4802610267 Å / SU ML: 0.147466455544 / Cross valid method: FREE R-VALUE / σ(F): 1.97613235845 / Phase error: 18.9889937889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.197895287896 3619 5.17613742008 %Random selection
Rwork0.164295533708 66298 --
obs0.165987919298 69917 88.8895951993 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.772994715 Å2
Refinement stepCycle: LAST / Resolution: 1.65000771809→31.4802610267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5731 0 205 737 6673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01589797504616088
X-RAY DIFFRACTIONf_angle_d1.412260745188312
X-RAY DIFFRACTIONf_chiral_restr0.0672310096811853
X-RAY DIFFRACTIONf_plane_restr0.006584923048471096
X-RAY DIFFRACTIONf_dihedral_angle_d21.68135995792135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.650008-1.67170.194190354862620.1716417772431284X-RAY DIFFRACTION45.0921273032
1.6717-1.69460.268642049179760.1735159773941490X-RAY DIFFRACTION51.209941138
1.6946-1.71880.182676268713770.1730297820671580X-RAY DIFFRACTION54.6864686469
1.7188-1.74450.232544888248900.1691089156871813X-RAY DIFFRACTION62.9715420251
1.7445-1.77170.2318515019821290.1781009017352012X-RAY DIFFRACTION71.2479201331
1.7717-1.80080.2201127127151440.1778208427772344X-RAY DIFFRACTION81.9499341238
1.8008-1.83180.2365943164011750.1843915610512731X-RAY DIFFRACTION96.1296725108
1.8318-1.86510.2135711818851750.1735492529422687X-RAY DIFFRACTION96.0402684564
1.8651-1.9010.2279243759381650.1773217658662803X-RAY DIFFRACTION96.3011031798
1.901-1.93980.2065244877861610.1709441739912756X-RAY DIFFRACTION96.3660389825
1.9398-1.9820.2090822669421800.1611572684692702X-RAY DIFFRACTION96.5170797053
1.982-2.02810.2233648237611940.1641376959132764X-RAY DIFFRACTION96.5719882468
2.0281-2.07880.1918808455651740.1579131112132750X-RAY DIFFRACTION96.8853545394
2.0788-2.1350.17381187561600.1527910347042790X-RAY DIFFRACTION97.0394736842
2.135-2.19780.200649251271500.1551147422142754X-RAY DIFFRACTION96.9292389853
2.1978-2.26870.1931993063561460.1584686881272806X-RAY DIFFRACTION97.1691902567
2.2687-2.34980.2089355249391200.1675544960462816X-RAY DIFFRACTION97.1542025149
2.3498-2.44380.194733839381120.1630095417872836X-RAY DIFFRACTION97.1974942301
2.4438-2.5550.2252419870441280.1781108626492816X-RAY DIFFRACTION97.6127320955
2.555-2.68960.1984632154191500.1810734533372811X-RAY DIFFRACTION97.8196233895
2.6896-2.8580.2099032937081540.1753815434262827X-RAY DIFFRACTION97.8339350181
2.858-3.07850.1997485458391690.1727864787062791X-RAY DIFFRACTION97.818902842
3.0785-3.3880.1965425815371730.1618761060792772X-RAY DIFFRACTION98.1666666667
3.388-3.87750.1555303246141210.1496810548492853X-RAY DIFFRACTION98.444223767
3.8775-4.88230.1509968705681280.1414533449372863X-RAY DIFFRACTION98.3234714004
4.8823-310.1868562402661060.1662236563422847X-RAY DIFFRACTION97.7167438782
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)
11.12931918681-0.657579666089-0.03741925732290.8944438545380.3862103684220.869883885763-0.005330763220750.0195127895939-0.022253463664-0.0830858625801-0.02249428390820.0832917038318-0.0167389698088-0.01608731056130.03512944697370.0430490145646-0.008871896005530.007173803380980.04561873820560.002980384232240.0376896134999-3.27376645724-21.50965233529.36711216239
23.312642704351.55648781231.08574439391.579490366160.1931786052751.378230783590.0656314949639-0.330389808476-0.09772529643420.138531751545-0.04501855964380.08822186470740.00400723806224-0.10231026657-0.009672923453770.0844038991856-0.004997617047330.007975367635630.06803906166650.003483609179730.0536461683684-8.24849565549-18.826584369915.5289110661
31.171586214891.60057534186-0.7977777079887.08868105487-3.67204256242.59817849187-0.0219886810148-0.173089895634-0.113836352460.482764950511-0.0575390394873-0.0100833673504-0.04326399968550.08738057314480.07458390656330.1797957385820.02553022468390.003677975751650.103800490897-0.0283331771320.07270718094493.75481333422-29.626979413124.3602102262
40.580804551378-0.3635446605850.1939696594192.69540504337-1.916628982.353895156680.0111102615637-0.0644553743101-0.03357988936160.1614298128160.02311225657340.1701481283240.0475743537748-0.0340210217902-0.06753692344280.099968949137-0.009782833049950.02108237617510.0474517001602-0.001257765406780.02956963079081.62841524255-29.011697203913.8059737376
53.60871096102-2.40583321494-2.835106784953.093276527572.422706150532.550430404940.0892175439253-0.1069519703070.3080233975480.1424796834130.032914219387-0.0462010476623-0.0124095345797-0.0232448192406-0.1054143296450.07375819290890.00630228998790.01088234153210.07107463069530.001092556136890.0667304817865-5.94425020535-4.6723717925114.7368361091
60.447147176498-0.288685460563-0.01567784835941.10107089589-0.3405169486490.562937913585-0.0351751288407-0.0816741325340.05076394460960.1210537144230.0150636093928-0.005268895459710.0203986242242-0.0236161548254-0.0002200748668220.0655549899112-0.011452637475-0.006119671350080.0871716400555-0.009431184535180.06425464139160.794294976665-23.811463818914.7715890435
71.54571718507-1.3086281682-1.021403650123.063261182731.149287741611.672318883380.1976645052330.1142521976620.226092120752-0.306030509827-0.0511614791316-0.222833502215-0.237521777875-0.00790779378821-0.1040658518130.07489770150670.010304425869-0.0123615194130.0771827046010.00907400690960.04667022217472.33410837999-14.40269342861.05699828134
81.365032767050.269687305464-0.2478047012790.970167139941-0.3154408094160.869540287741-0.0253681613625-0.0234800336572-0.0823904554524-0.02742737378360.04069179307270.0665176186990.0244866074419-0.120929407659-0.01487033811850.02613602178440.00235176630223-0.0002725395125860.048789992319-0.002248796204090.0468758530946-13.6414195656-9.06061535015-20.6787255647
91.06797941888-0.6441940999420.3981174708782.252245885790.209871729883.740217668820.02853644624490.285551853407-0.335950983664-0.442433157866-0.104392100160.197029544480.489225575027-0.2263438181370.01489442184510.160277727656-0.02795616778860.02642666706130.134395282084-0.05085964756830.16736367539-6.39696242734-21.7716665345-33.0783208404
100.768790518660.318702266186-0.4877859333120.766487576122-0.3139791545961.561672062550.053030047244-0.0585037320694-0.002390421812840.0424117772126-0.04807518356550.0498556173203-0.002017522845670.00606984725053-0.009313496038470.01978491936530.0085027392954-0.01215639799140.0409751931314-0.001019264766570.0420655599519-10.3483784676-9.96732704748-13.7899260626
113.02121033459-2.622661753391.832059289444.31983063233-0.3951741086471.807579980.0698783149317-0.182392116394-0.2916218061870.2152466070950.1355196975950.2051025906670.185822863796-0.314614097235-0.08036579729880.119080346594-0.0350898652701-0.01759964560720.1640327555210.03604957581360.115518137552-11.7705288057-23.8957189523-4.71755528665
120.4461910109720.298700368114-0.1570309598931.09651947545-0.5951720581651.19379554641-0.02622760998410.0428360668863-0.0483331238127-0.1875557228780.0331913076449-0.08510079924670.1236778031820.0785459489561-0.003823574974940.05849753018080.00494020943419-0.003357356862630.06126720542670.005099382045530.0558892418516-4.5435695032-8.02559936071-28.4904137486
131.249167528830.867772075181-1.184055452531.49696926252-1.446606743732.561995244240.0405321873449-0.1193819377120.07590041856910.22223790678-0.04742841628980.000344019965688-0.2873238586860.0271417436808-0.04017135130820.07236503513940.0125333768151-0.007751133878350.0551471223172-0.009542038474550.0517975602783-6.270381270310.533930975481-13.44590741
141.12190424129-0.1441038631970.2013958374461.42438708399-0.3812194982610.830379492158-0.01289736551750.008952967713460.006624534361630.01388940743110.02893961726230.153893436735-0.0218721104723-0.0401238959835-0.006817189040140.03231408758910.00135137731410.002777644011190.0544987396787-0.001406387974590.04031412146783.2161042476810.41713216622.8167160505
150.8306930833-0.0191225392288-0.01388512196032.110093641581.165339580882.869665916070.00776425873899-0.06569957542050.1150343262880.0877415874444-0.0191167260261-0.0161371759702-0.149684245551-0.02404962228540.009248739825830.04125667437820.007799863989-0.008747533303330.06369946560910.00837240352830.047871442695110.596752922917.677306597631.8788783275
160.28717286051.11027281938-0.5547599362195.47778921409-2.135753804731.02128344766-0.0217542219254-0.03252592562620.0719046298622-0.7067835477490.2127295041810.4090846860420.223999902085-0.245274843049-0.2229151949710.147529876986-0.0120063757462-0.02702310452930.1110153158860.0007414701834290.08770453970552.6108668518818.39632776294.8102531141
170.0943536798659-0.1754740041540.1023637391190.644684074379-0.3889151914880.725423103345-0.01019280942270.01801995052330.04390999188120.0163563538573-0.0065328321842-0.0243857494496-0.05791167910980.0453161003190.01266737092740.0475347746724-0.00378945018230.009402128600770.06629916703080.003401439969850.06256024646611.157198897912.739937241325.3209682094
181.37538387086-1.083818968431.038302496082.40313824071-1.566479381562.884329039810.1495618219690.248255378444-0.147658011998-0.362906510881-0.1227411896020.058812971520.2982049885820.171422963558-0.06611524664450.106729706397-0.009972599794950.009405645065880.0844622711008-0.003891981385520.070209734748310.5585099740.78044687686715.3077527258
190.7477309257670.4253100176640.01020044275131.279738513450.2890468644960.877661849581-0.004763820095220.03870135665640.0458476201050.103843703567-0.04706347529050.09423018533930.0711035119797-0.009717022728150.04723134293540.04635036955260.00413581938330.005216436829350.0561937878608-0.004383029584580.0540743940744-21.441497820821.3763597716-9.30700227828
202.81735305605-2.080926551570.9000125922177.84440852547-3.563923243393.94153130911-0.04301569215820.1831042315580.385735352343-0.485440862332-0.130458567787-0.0304260601073-0.09928753629160.2209131997710.1385312680410.146965199389-0.0268436082019-0.03139312602660.08784372454480.004866167403020.0994967166592-14.343944988630.9948690467-22.3859855565
211.285475039190.0233619126391-0.04205370216652.46547788368-0.05424413576391.34033483820.005929331911970.1093802307680.117341560676-0.158687708377-0.07372742883850.1774610246330.08093878798110.0290888079322-0.05037041848760.0766463278987-0.00689468443622-0.02999523576550.0411974031814-0.005678773055940.0810862304937-16.091747375830.1477824347-11.7112731938
223.141937023092.453432306722.251855649392.715360449941.9923815641.676951126570.05245777346480.0639666268393-0.1096371917560.125764939960.0447360879508-0.0547203523954-0.057545435071-0.0225564982024-0.07786549185240.0810443766849-0.007566277276430.00639015176170.05779575017660.002977849480540.0684961424287-22.68493671875.77316461478-13.143266808
230.5252358327930.4896317195690.1613759226740.982117679136-0.1921179196860.932068466510.007682667061410.05347148023580.01226606903950.00878398117111-0.036690778795-0.0197206010392-0.004235395188810.02260199139960.02607701963520.03759687981210.02508661063740.006640994600990.06892957455190.003960736149990.0766070712401-16.457439263525.1598938905-12.8415819353
240.5158053058650.022573064209-0.2058113818433.032662852561.775105593261.318984113510.0049356309656-0.220443267135-0.08375728336540.5533237373490.23516019518-0.06537534428690.5332040224480.192613046950.01365541364810.2038336552750.013360491092-0.03677088043770.114755796160.01919370656390.0866127350583-9.8125874156321.7816276514.28933371094
255.30115288872-3.085418509651.743075007313.262949952830.5547046847112.56388537256-0.144532747783-0.0279377309717-0.7263494936660.4009662736540.1828777495450.1296154711210.143521995303-0.168168261603-0.05384572403470.147670233784-0.02461961274664.36504194224E-50.07533596116640.02182782671360.10913996584-20.14131989576.38608429863-5.1397217345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 96 )
5X-RAY DIFFRACTION5chain 'A' and (resid 97 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 162 )
7X-RAY DIFFRACTION7chain 'A' and (resid 163 through 180 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 56 )
9X-RAY DIFFRACTION9chain 'B' and (resid 57 through 83 )
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 111 )
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 126 )
12X-RAY DIFFRACTION12chain 'B' and (resid 127 through 162 )
13X-RAY DIFFRACTION13chain 'B' and (resid 163 through 180 )
14X-RAY DIFFRACTION14chain 'C' and (resid 2 through 56 )
15X-RAY DIFFRACTION15chain 'C' and (resid 57 through 96 )
16X-RAY DIFFRACTION16chain 'C' and (resid 97 through 114 )
17X-RAY DIFFRACTION17chain 'C' and (resid 115 through 162 )
18X-RAY DIFFRACTION18chain 'C' and (resid 163 through 180 )
19X-RAY DIFFRACTION19chain 'D' and (resid 0 through 56 )
20X-RAY DIFFRACTION20chain 'D' and (resid 57 through 76 )
21X-RAY DIFFRACTION21chain 'D' and (resid 77 through 96 )
22X-RAY DIFFRACTION22chain 'D' and (resid 97 through 111 )
23X-RAY DIFFRACTION23chain 'D' and (resid 112 through 162 )
24X-RAY DIFFRACTION24chain 'D' and (resid 163 through 172 )
25X-RAY DIFFRACTION25chain 'D' and (resid 173 through 180 )

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