PDB-7u6z: Pertussis toxin E129D NAD

ID or keywords:

Entry

Database: PDB / ID: 7u6z

Title

Pertussis toxin E129D NAD

Components

Pertussis toxin subunit 1

Keywords

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

Function / homology

Function and homology information

Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ ADP-ribosyltransferase activity / nucleotidyltransferase activity / toxin activity / extracellular region
Similarity search - Function

Biological species

Bordetella pertussis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.30001992416 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	Mar 6, 2022	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	7u6z.cif.gz	178 KB	Display	PDBx/mmCIF format
PDB format	pdb7u6z.ent.gz	123.2 KB	Display	PDB format
PDBx/mmJSON format	7u6z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7u6z_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	7u6z_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7u6z_validation.xml.gz	18.4 KB	Display
Data in CIF	7u6z_validation.cif.gz	26.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u6/7u6z ftp://data.pdbj.org/pub/pdb/validation_reports/u6/7u6z	HTTPS FTP

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Related structure data

Related structure data	7skiC 7skkC 7skyC 7sneC 1bcpS C: citing same article (ref.) S: Starting model for refinement
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

B: Pertussis toxin subunit 1

A: Pertussis toxin subunit 1

hetero molecules

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

1

B: Pertussis toxin subunit 1

hetero molecules

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

2

A: Pertussis toxin subunit 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	69.190, 34.560, 71.760
Angle α, β, γ (deg.)	90.000, 90.000, 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: 20727.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: ptxA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P04977, Transferases; Glycosyltransferases; Pentosyltransferases, NAD+ ADP-ribosyltransferase
#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.07 Å³/Da / Density % sol: 40.57 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / Details: 0.2M KI, 25% PEG3350 / Temp details: room temperature

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.3→25 Å / Num. obs: 64240 / % possible obs: 76.3 % / Redundancy: 4.8 % / B_iso Wilson estimate: 10.1641427435 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.026 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.3→1.37 Å / Mean I/σ(I) obs: 5.2 / Num. unique obs: 4829 / CC_1/2: 0.917 / R_pim(I) all: 0.153

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1BCP

1bcp

Resolution: 1.30001992416→24.4499753323 Å / SU ML: 0.114714879346 / Cross valid method: FREE R-VALUE / σ(F): 1.33679855444 / Phase error: 22.3331931016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.213748167576	3268	5.10098960447 %	Random selection
R_work	0.193617840545	60798	-	-
obs	0.194662102267	64066	76.1991983539 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.1323662221 Å²

Refinement step

Cycle: LAST / Resolution: 1.30001992416→24.4499753323 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2706	0	90	286	3082

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0075861352654	2872
X-RAY DIFFRACTION	f_angle_d	1.13287756552	3922
X-RAY DIFFRACTION	f_chiral_restr	0.0798589042945	398
X-RAY DIFFRACTION	f_plane_restr	0.00645139289546	518
X-RAY DIFFRACTION	f_dihedral_angle_d	24.8016406513	1010

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 (%)
1.30002-1.3194	0.223608364707	55	0.21463552382	1104	X-RAY DIFFRACTION	32.0786050374
1.3194-1.34	0.200520494596	73	0.208431315757	1337	X-RAY DIFFRACTION	39.1014975042
1.34-1.362	0.224378075928	91	0.214377752833	1495	X-RAY DIFFRACTION	43.9213514262
1.362-1.3855	0.268975549615	99	0.243760550491	1728	X-RAY DIFFRACTION	49.5390455531
1.3855-1.4107	0.220594029342	108	0.203230086319	1974	X-RAY DIFFRACTION	58.3683767872
1.4107-1.4378	0.245840278823	110	0.209369291033	2322	X-RAY DIFFRACTION	66.3755458515
1.4378-1.4672	0.242589346725	83	0.212953226305	1811	X-RAY DIFFRACTION	52.2482758621
1.4672-1.4991	0.200810194309	83	0.205823666376	2093	X-RAY DIFFRACTION	59.4210813763
1.4991-1.5339	0.217134561863	129	0.19903700334	2318	X-RAY DIFFRACTION	92.4442765395
1.5339-1.5723	0.210559751531	206	0.186545133223	3408	X-RAY DIFFRACTION	99.7240618102
1.5723-1.6148	0.216037227869	198	0.181705258678	3387	X-RAY DIFFRACTION	99.4176372712
1.6148-1.6623	0.211312932815	224	0.174447267782	3440	X-RAY DIFFRACTION	99.592280511
1.6623-1.7159	0.175789883754	172	0.183812511564	3447	X-RAY DIFFRACTION	99.5050866098
1.7159-1.7772	0.189172032908	173	0.189666969655	3438	X-RAY DIFFRACTION	99.476584022
1.7772-1.8484	0.215780340536	142	0.184779716361	3485	X-RAY DIFFRACTION	99.4516040581
1.8484-1.9325	0.23387490717	101	0.193319960918	2206	X-RAY DIFFRACTION	77.6767676768
1.9325-2.0343	0.203337108959	150	0.187507174838	2882	X-RAY DIFFRACTION	83.8495575221
2.0343-2.1617	0.208495651526	175	0.19030522941	2969	X-RAY DIFFRACTION	85.9721082855
2.1617-2.3285	0.207477985962	169	0.193669357181	2943	X-RAY DIFFRACTION	85.7300275482
2.3285-2.5626	0.237351559087	203	0.198945535548	3469	X-RAY DIFFRACTION	99.512195122
2.5626-2.9328	0.232376260598	196	0.198837908167	3272	X-RAY DIFFRACTION	93.5275080906
2.9328-3.693	0.194095861453	153	0.190860965039	3211	X-RAY DIFFRACTION	93.6264959644
3.693-24.44	0.213991866656	175	0.195739071631	3059	X-RAY DIFFRACTION	84.6818538885

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	1.1639354205	-0.0982709359136	0.3431994934	1.71064764219	-0.230562063601	1.66779278651	0.01889428956	0.0332593693892	-0.088285675383	-0.0261172985476	-0.0232775006805	-0.113850565113	0.149008036002	0.0413719338023	0.00605679338036	0.058300568147	-0.00132191383634	0.00270895254815	0.0615278096214	-0.00366395811612	0.0607607020538	-24.5024320025	-4.41946402915	-21.3995623645
2	2.6837414757	0.0659666835677	-1.10063770734	0.973782841712	-0.268839855496	2.22090892633	-0.0149539655191	0.239811861295	0.0419247226468	-0.147008139864	-0.0534702716732	-0.176831853509	0.0753103023633	0.24924493424	0.0197960015447	0.0711702448397	0.0169966301815	0.0122218331703	0.121815784348	0.0271589115755	0.0701171286226	-17.0466301001	3.11094181736	-30.6393537141
3	1.54775460204	-0.769428152479	1.39955359656	0.835659283163	-0.420811933791	2.45435995148	-0.0867462367271	-0.101830837065	-0.0115725426597	0.205102342242	0.0450714878534	-0.128745542679	0.0193161168681	0.0894299178624	0.0439476146617	0.106605200224	0.00723506599255	-0.0233342044193	0.0789150383907	0.0141161739209	0.0719134552568	-22.5761702609	-3.89727197412	-9.81979136242
4	3.85560865147	0.435803124683	-3.81597674576	0.719501506692	-0.377721408737	4.17274659184	0.0264942634318	0.254650810528	0.174793705556	-0.0733082077401	-0.0293832820584	0.00982168883118	-0.169224794685	-0.0615567112671	-0.00063092053143	0.0646840508307	-0.0076566977301	-0.0225154391121	0.111293044974	0.0366198586659	0.0588642347826	-28.4776408077	6.18897118839	-30.9200706044
5	4.56691688272	-1.00676185352	-3.66008908052	0.908533433722	1.31626378261	3.30669743449	0.265743633723	0.349053982606	0.545467385141	-0.254512998171	0.0279731182218	-0.203107930383	-0.3205718264	0.210302174939	-0.301520481863	0.164889299357	0.00797692198814	0.0324690003537	0.299602352247	0.0966148351589	0.178892177451	-20.7707669563	9.92292945043	-40.370351814
6	1.73965218032	-0.92665497404	0.970144670711	1.81210076415	-1.04789743296	1.8747064336	-0.069365036093	-0.132577854696	-0.0463708527732	0.201510704895	0.0730075158496	0.0992269084089	-0.0646281741465	-0.184661335624	-0.0176315910946	0.0905327325337	-0.0092186792759	0.0106241114489	0.0980738247505	-0.00347292873848	0.075165624575	-34.3223699306	2.81981023115	-14.4337219895
7	0.687343707182	-0.660057998974	-0.0900658156285	1.51478348032	0.208178754249	1.2079554696	0.0290764690036	-0.0836286640472	-0.0929861899261	0.0166631360794	-0.0322584449646	0.0669555054438	0.0416245613103	-0.189802890538	0.00474466108298	0.0480979968511	-0.0226308331314	0.0177629627854	0.121190873077	-0.0148044165052	0.0877893250452	-56.2309544464	-11.2516568514	-8.92240387017
8	1.73655875633	0.996888904215	-0.0703286944278	3.48269318866	-0.604818749863	1.43124972209	-0.0197983525181	0.200366975566	-0.131589389677	-0.11088876278	-0.0319514313328	0.11252476011	0.168000440994	-0.078407524621	0.0477607744798	0.0737693616059	-0.00573697370393	0.00554237762678	0.0910801618916	-0.0250588271113	0.104481446099	-53.5127834577	-15.9015122405	-15.182773124
9	6.03353956285	1.19480525752	3.85160873418	1.16538625947	0.476267286372	3.69465229291	-0.0787451598443	0.403515969838	0.157936983567	-0.0691379997546	0.0166897203776	0.213857738849	-0.230621357564	-0.0774989371676	0.0443977109956	0.124932671121	0.0548538670545	0.0166916157469	0.193204890829	-0.0174038753544	0.149082667871	-64.1919973633	-4.03748100896	-23.6544469001
10	2.9268588112	0.507109440499	1.20361676054	2.45800928411	-0.260865433172	4.10545530449	-0.197341021882	-0.255873029569	-0.0596979525092	0.260457218536	-0.0837318687971	-0.0209936111264	0.135882138652	-0.215796085567	0.231263760928	0.277722480587	0.0683645921323	-0.163653741985	0.524778184417	-0.00801193258888	0.372638323624	-75.3976368004	-10.7919115102	-27.0609287903
11	1.75034627342	0.0151707244011	0.483573806318	1.0110566097	0.0394945411007	1.95077221631	-0.0197400471605	-0.0871329726018	0.11029432899	0.0496654173173	-0.0404662508893	0.120897170808	-0.107650876887	-0.220609367203	0.0472066273316	0.0695400718863	0.00345323480928	0.0201900837937	0.113075053056	-0.011930329087	0.0854651936907	-58.661221993	-4.78141756368	-7.52758255185
12	2.25813376603	-1.98567527234	-2.05730164476	2.92637586609	2.19140896551	2.18283306968	0.0255551054798	0.0571839674982	-0.0301155818828	-0.0225757154253	0.0122033936558	-0.170959331245	0.10239014542	0.00306458117387	-0.0404823613605	0.0655462808135	0.00381941393827	-0.00589331506174	0.079530823287	-0.00615983473297	0.104286293757	-39.4385551127	-13.8127226304	-14.2362045579
13	1.93370534341	-1.6866874583	-0.847052088291	2.1709954679	1.41586137955	1.68108054471	0.067360011535	0.0986516382005	0.0526973489154	-0.154714399609	-0.0473299375564	-0.0478292894888	-0.0715342116834	-0.00145577669523	-0.01165368913	0.0908840111817	-0.010033430635	0.00494144474928	0.0960045276766	0.00286313335395	0.110164220538	-48.0933834827	-12.0732941039	-11.4079004109
14	3.77206279297	-0.404993619018	3.56239202168	0.642246081252	-0.624499681857	3.46824764325	0.0605356284451	-0.0370255711909	0.0777997399644	-0.0182124592777	-0.0422385456303	0.208123879786	-0.219694628425	-0.521660839274	-0.022705214372	0.109594747312	0.0596378772526	0.0279136296573	0.284999314826	-0.0399384953406	0.156100419955	-65.00426483	-2.02014592715	-7.53398874765
15	1.32969769677	0.757324522433	1.50003534318	0.846995705038	0.137501338318	2.93241732156	0.0532677768343	0.177747278749	0.0154997215833	-0.110458084169	0.148870271545	0.322096191661	-0.178337164735	-0.202194761805	0.075957413165	0.325619974864	0.323318313992	-0.131625439785	0.62108841168	-0.127674005465	0.31460329046	-73.9183778674	1.67837714624	-15.8158110319
16	7.11585635444	-0.311893096118	0.154197360834	1.72992402052	0.2602433261	1.92398812517	-0.0985703209894	-0.349291969499	0.00140433416044	0.381497715036	0.0524105768454	0.106406453712	-0.0282285305953	-0.0852196663992	0.0252557140188	0.175274226249	-0.0283291896752	0.0328864745708	0.251006199431	-0.0735554868206	0.1247992735	-55.0412536991	-1.30006701756	3.72768424957
17	4.58675716629	1.56402107484	-0.385752073155	1.7578436816	0.654181060917	2.61014059367	0.148263973731	-0.157714698661	-0.339998632121	0.0297871473917	-0.0497999536138	-0.721745838262	0.118066553667	0.214215726881	-0.10078659441	0.089781625074	-0.00576897886501	-0.016859019907	0.129009474906	0.0281916017795	0.160225583415	-40.3505147858	-11.7763576881	-6.09083799939

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 56 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 57 through 96 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 97 through 137 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 138 through 149 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 150 through 162 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 163 through 180 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1 through 36 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 37 through 56 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 57 through 76 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 77 through 83 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 84 through 96 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 97 through 111 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 112 through 137 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 138 through 149 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 150 through 162 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 163 through 172 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 173 through 180 )

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About Yorodumi

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Yorodumi