PDB-7ski: Pertussis toxin in complex with PJ34

ID or keywords:

Entry

Database: PDB / ID: 7ski

Title

Pertussis toxin in complex with PJ34

Components

Pertussis toxin subunit 1

Keywords

TOXIN / TRANSFERASE/INHIBITOR / ADP-RIBOSYLTRANSFERASE / TRANSFERASE / WHOOPING COUGH / INHIBITOR / PERTUSSIS / TRANSFERASE-INHIBITOR complex

Function / homology

Bordetella pertussis toxin A / Pertussis toxin, subunit 1 / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / extracellular region / Chem-P34 / Pertussis toxin subunit 1

Function and homology information

Biological species

Bordetella pertussis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.09912437248 Å

Authors

Littler, D.R. / Beddoe, T. / Pulliainen, A. / Rossjohn, J.

Funding support

Australia, 1items

Citation

Journal: 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

Deposition	Oct 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Apr 20, 2022	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	May 18, 2022	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ski.cif.gz	188.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7ski.ent.gz	130.7 KB	Display	PDB format
PDBx/mmJSON format	7ski.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ski_validation.pdf.gz	882.1 KB	Display	wwPDB validaton report
Full document	7ski_full_validation.pdf.gz	887.8 KB	Display
Data in XML	7ski_validation.xml.gz	20.5 KB	Display
Data in CIF	7ski_validation.cif.gz	30.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/7ski ftp://data.pdbj.org/pub/pdb/validation_reports/sk/7ski	HTTPS FTP

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Related structure data

Related structure data	7skkC 7skyC 7sneC 7u6zC 1prtS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#69 - Sep 2005 Cholera Toxin similarity (3)

Deposited unit

A: Pertussis toxin subunit 1

B: Pertussis toxin subunit 1

hetero molecules

41.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pertussis toxin subunit 1

hetero molecules

defined by author
Evidence: gel filtration
20.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pertussis toxin subunit 1

hetero molecules

defined by author
20.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	59.369, 42.541, 72.775
Angle α, β, γ (deg.)	90.000, 95.789, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Pertussis toxin subunit 1 / PTX S1 / Islet-activating protein S1 / IAP S1 / NAD-dependent ADP-ribosyltransferase Mass: 20410.965 Da / Num. of mol.: 2 / 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-P34 / N~2~,N~2~-DIMETHYL-N~1~-(6-OXO-5,6-DIHYDROPHENANTHRIDIN-2-YL)GLYCINAMIDE Mass: 295.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₇N₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.08 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.15M NaCl, 0.1M Tris(hydroxymethyl)aminomethane pH 8.0, 8% w/v PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 1994 / Details: NULL
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.099→21.831 Å / Num. obs: 142710 / % possible obs: 96.9 % / Redundancy: 5 % / B_iso Wilson estimate: 9.42339965695 Å² / CC_1/2: 0.994 / R_pim(I) all: 0.046 / Net I/σ(I): 8.6
Reflection shell	Resolution: 1.1→1.16 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 19609 / CC_1/2: 0.746 / R_pim(I) all: 0.366

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Processing

Software

Name	Version	Classification
PHENIX	1.10.1_2155	refinement
PHENIX	1.10.1_2155	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PRT

1prt

Resolution: 1.09912437248→21.8309394753 Å / SU ML: 0.0937900205365 / Cross valid method: FREE R-VALUE / σ(F): 1.3379110568 / Phase error: 17.2879651582
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.178366623841	7080	4.96173576655 %	Random selection
R_work	0.171050461298	135612	-	-
obs	0.171413573292	142692	97.065425901 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 17.7801999968 Å²

Refinement step

Cycle: LAST / Resolution: 1.09912437248→21.8309394753 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2830	0	44	422	3296

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0128979184846	2973
X-RAY DIFFRACTION	f_angle_d	0.91581441307	4052
X-RAY DIFFRACTION	f_chiral_restr	0.0705289773054	409
X-RAY DIFFRACTION	f_plane_restr	0.00541852269681	544
X-RAY DIFFRACTION	f_dihedral_angle_d	23.2867324468	1070

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.1-1.1116	0.242454491331	211	0.241405413743	3935	X-RAY DIFFRACTION	85.4316917371
1.1116-1.1247	0.246402234234	250	0.222728377366	4413	X-RAY DIFFRACTION	94.6802030457
1.1247-1.1384	0.243030623145	241	0.207634163414	4382	X-RAY DIFFRACTION	95.2802967848
1.1384-1.1528	0.213252058822	227	0.202881631443	4393	X-RAY DIFFRACTION	94.5171849427
1.1528-1.168	0.212336256607	242	0.200620074689	4381	X-RAY DIFFRACTION	95.9925249169
1.168-1.184	0.203085716332	250	0.197814627425	4399	X-RAY DIFFRACTION	94.7808358818
1.184-1.2009	0.191992965981	224	0.192811791336	4458	X-RAY DIFFRACTION	96.2384378212
1.2009-1.2188	0.202756784152	228	0.190115474256	4475	X-RAY DIFFRACTION	95.6283041887
1.2188-1.2379	0.19533016672	238	0.189903902293	4448	X-RAY DIFFRACTION	96.3800904977
1.2379-1.2582	0.184911876591	211	0.192357608577	4484	X-RAY DIFFRACTION	96.4858199753
1.2582-1.2798	0.203971907108	221	0.185823246069	4484	X-RAY DIFFRACTION	96.334971335
1.2798-1.3031	0.189967585597	231	0.180931274098	4482	X-RAY DIFFRACTION	96.975308642
1.3031-1.3282	0.181373677825	244	0.18174618357	4493	X-RAY DIFFRACTION	96.4569334148
1.3282-1.3553	0.184274611411	242	0.178882446861	4512	X-RAY DIFFRACTION	97.5379565039
1.3553-1.3848	0.19624456908	254	0.180526705202	4494	X-RAY DIFFRACTION	97.3748974569
1.3848-1.417	0.176152201484	227	0.172405841652	4523	X-RAY DIFFRACTION	96.8992248062
1.417-1.4524	0.182661167044	208	0.167322138334	4584	X-RAY DIFFRACTION	98.1967213115
1.4524-1.4916	0.182446092069	222	0.170919371653	4549	X-RAY DIFFRACTION	98.0879934211
1.4916-1.5355	0.18796292069	245	0.16147984988	4526	X-RAY DIFFRACTION	97.8666666667
1.5355-1.5851	0.171221514889	232	0.162769325444	4590	X-RAY DIFFRACTION	97.9683055668
1.5851-1.6417	0.155049089975	229	0.160093766077	4599	X-RAY DIFFRACTION	98.3099165139
1.6417-1.7074	0.166186579443	254	0.161521537046	4561	X-RAY DIFFRACTION	98.7894952811
1.7074-1.7851	0.188105508847	246	0.164951743225	4637	X-RAY DIFFRACTION	99.0064882401
1.7851-1.8792	0.190391929992	229	0.171322356241	4610	X-RAY DIFFRACTION	99.0786240786
1.8792-1.9968	0.178372118031	225	0.164944748706	4637	X-RAY DIFFRACTION	98.7408610885
1.9968-2.1509	0.16148987355	268	0.164618319735	4639	X-RAY DIFFRACTION	99.5738636364
2.1509-2.3671	0.177087304113	234	0.161371750276	4688	X-RAY DIFFRACTION	99.1938734381
2.3671-2.7091	0.170800229055	246	0.177608825463	4685	X-RAY DIFFRACTION	99.9797242498
2.7091-3.411	0.182902802553	250	0.166673724089	4710	X-RAY DIFFRACTION	100
3.411-21.8	0.152575912369	251	0.156658760142	4841	X-RAY DIFFRACTION	99.86271818

Refinement TLS params.

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

ID	L11 (°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)
1	1.00818413852	0.509750571459	0.245073869899	0.621753520316	0.15875282141	1.58659388204	-0.0391174009767	-0.0158335814106	-0.0186363908431	-0.0511379510222	0.0138078489606	0.11296709398	-0.0697209797943	-0.0530386012316	0.0187704187438	0.0731005346689	-0.00379731945858	-0.00719735605133	0.032897249661	-0.00694829068355	0.0609660679063	14.9615655746	-2.19830726626	77.9437943301
2	2.56847549896	1.44132235442	0.0935270449523	1.65730201852	0.16254175945	0.719756940191	-0.0690427842014	0.097006363326	-0.156652268265	-0.0724786645616	0.0520429268093	-0.0417014272059	0.0169425835131	0.0381356468946	0.0233779020788	0.086915346531	0.00662182239862	0.00423061883761	0.0535097047026	-0.00708985321644	0.0717277809282	17.129894145	-11.5077492073	71.8460853489
3	4.96597370148	0.151022905526	-0.181077552486	4.17144943088	0.819303102111	4.77555493123	-0.0219752456163	-0.201300743209	-0.48597919129	0.155057760407	-0.100428884626	-0.00924927942293	0.402809366307	-0.0154813122555	0.0923539465026	0.143219895539	-0.013548526084	0.0147677035062	0.0993705779904	0.00491029186368	0.151005401555	4.12696796636	-17.4322878974	80.8646367102
4	1.38924707524	0.354043430269	0.212684822676	0.813915744168	1.10567366996	1.57110824192	-0.0373140974288	-0.0915340446919	-0.249894654293	0.191938003112	0.0395188746184	0.0574535269192	0.214078268718	0.0250427771556	0.00963363919406	0.100426581929	0.0118951493624	0.0117540927687	0.048513084218	0.00594811512258	0.109926073594	10.1843942325	-13.7312318893	78.4987412134
5	1.94505131031	-1.33443913111	1.16629373396	1.36231054775	-0.876630777162	1.37485506388	-0.0286869730719	-0.132288199987	0.00616985946589	0.0838750008635	-0.0109318439608	-0.052965619678	0.0082032058183	0.0287475337468	0.0285489142209	0.0867637005154	0.00245937094101	0.00782015151774	0.105089333527	0.0142092209557	0.0760369570695	20.8277277568	-7.21900450856	91.7393784455
6	1.21587489249	0.0791418905624	0.484108345343	0.907227273317	-0.0874277403779	1.26483984786	-0.0967556846535	0.0117270001834	0.00309287461667	0.040927002833	0.000266782609945	-0.0325735352786	-0.058641778349	0.102632785535	0.0410253620177	0.0569760985097	0.00486893547698	0.0188745175539	0.040485906754	-0.00100520297009	0.0528609491282	21.2246073752	-6.14920340234	80.7397760015
7	1.65579176056	1.12863125724	-0.623059369887	1.27918061012	-0.497297007461	1.00467043128	0.0640729324765	0.0242363158517	-0.0170016173878	-0.186127762046	0.0563488119585	0.414697623541	0.160097424034	-0.311442048916	-0.0432893941679	0.0906559075601	-0.0234576640947	-0.0461517713538	0.127729881763	-0.00215370191389	0.226321228505	-3.98057197581	-9.46180561951	77.3410228098
8	1.65771209849	0.547226806679	1.44735683561	0.180777293688	0.479812351163	1.2592027451	0.38056159053	-0.279370733184	-0.613157706071	0.256537375345	0.0276013627088	0.509634064483	0.690778497841	-0.749843753597	-0.216385507474	0.387777288175	-0.105021906762	-0.00956411199835	0.285453569401	0.017384645208	0.470098964361	-6.41051907693	-15.7645468692	87.4104117276
9	0.741840488447	-0.311912072247	-0.748338835674	0.546491149273	0.555009404128	1.90767512647	0.0416143267566	-0.0474057685211	0.0107290459387	0.0020533323557	-0.0459150451997	0.0993526024105	-0.0370697103511	-0.152302373439	0.0130209116074	0.0742615370266	-0.00284379668911	0.00908435780337	0.0860781666655	-0.0191226663408	0.0910455197522	3.80949919671	-5.50995537816	82.2197556844
10	0.809018785597	0.245003510132	0.0416681630769	0.831315263787	0.00831440828193	0.391078348362	-0.0760962737779	0.0571223368776	-0.00320520950829	-0.0656160245215	0.0212931481778	0.0180018529938	-0.0594061107372	0.0522730535671	0.0479723190511	0.057124034932	-0.00750227804141	0.00658678652214	0.0328451460184	0.00568804845854	0.0488145459394	21.4920911695	-2.50871982012	75.6137845183
11	0.24115604633	-0.477936495851	1.02269773423	1.55928062257	-2.41826361598	4.48177256107	-0.0934757601943	-0.0895201388552	0.0253606391162	0.310294888323	-0.0688053015671	-0.133703123616	-0.353342336898	0.131998210737	0.114744814353	0.139826385605	-0.0177433220046	-0.0309035952919	0.138047349689	0.0323860735835	0.0931499544395	31.196478018	-0.129230051309	87.4787833796
12	2.75131685972	0.706636764164	-0.213024090649	0.954842454798	-0.290682124234	0.857408438639	-0.174772877448	0.398182774721	0.132328028716	-0.181531779805	0.121585004843	0.18058440699	-0.133376541528	-0.10347672205	0.0620144741754	0.126780868827	-0.00208152616406	-0.0344750014942	0.0876998604001	-0.00878745683214	0.103490511901	8.75761918748	0.436088444455	68.1968272065
13	1.37698166018	-0.886178293635	0.0541302758379	0.929738520313	-0.252538212661	1.33127585088	-0.0788421029392	-0.0651112734544	-0.191666408646	0.0165794074299	0.0390475474197	0.137608079974	0.118045451259	-0.0346599663414	0.038538078956	0.0912890831241	-0.0129213773724	0.0198556619075	0.116227377926	-0.0204328113308	0.10326390184	0.120638048383	-1.60473353303	105.672715989
14	1.79621557156	0.655645691394	0.37099762961	0.603387722696	0.103328003892	0.561316239015	-0.121767292082	0.126021856013	-0.175596613955	-0.110235760445	0.113412280543	0.0194863169182	-0.0548231621242	0.00828816700351	0.00269786617471	0.0866451006132	-0.00540946967042	-0.000802078946844	0.124115790231	-0.0207839829558	0.129583282982	-8.73640387874	1.68797165998	91.6128489163
15	0.782482998478	-0.365215999294	-0.331085131885	0.300871890897	0.364946788184	1.58059202586	-0.0515891137957	-0.0692110446141	-0.0709102934115	0.0567265673724	-0.0180831235176	0.0472488144211	0.183467777838	0.074315056693	0.0744235094684	0.108382956696	-0.00190075611873	0.0187242613867	0.107129391396	-5.66822712375E-5	0.0965725759119	9.56000718077	-6.39821598564	100.510276655
16	0.97386504451	0.289532667495	-0.0371610815648	1.28787510523	0.378691158253	1.0584739438	-0.136073760645	-0.0998009765631	0.189454793314	-0.079573346036	0.0166607931627	0.0505701312398	-0.199426907286	-0.0581323008304	0.081720229102	0.0986065449193	-0.0083349236124	0.00877712118704	0.101071317661	-0.0118317348454	0.0698622185702	-2.50536552756	9.891915681	102.346548721

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 31 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 32 through 41 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 42 through 56 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 57 through 76 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 77 through 96 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 97 through 111 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 112 through 119 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 120 through 133 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 134 through 150 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 151 through 162 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 163 through 180 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2 through 56 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 57 through 92 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 93 through 137 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 138 through 180 )

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi