PDB-7ri3: Crystal structure of Albireti Toxin, a diphtheria toxin homolog, ...

ID or keywords:

Entry

Database: PDB / ID: 7ri3

Title

Crystal structure of Albireti Toxin, a diphtheria toxin homolog, from Streptomyces albireticuli

Components

Diphtheria_T domain-containing protein

Keywords

TOXIN / diphtheria toxin / DT / homolog / Streptomyces albireticuli

Function / homology

Function and homology information

NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space / metal ion binding
Similarity search - Function

Biological species

Streptomyces albireticuli (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.69 Å

Authors

Sugiman-Marangos, S.N. / Gill, S.K. / Melnyk, R.A.

Funding support

Canada, 1items

Citation

Journal: Commun Biol / Year: 2022
Title: Structures of distant diphtheria toxin homologs reveal functional determinants of an evolutionarily conserved toxin scaffold.
Authors: Sugiman-Marangos, S.N. / Gill, S.K. / Mansfield, M.J. / Orrell, K.E. / Doxey, A.C. / Melnyk, R.A.

History

Deposition	Jul 19, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 2, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 16, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ri3.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb7ri3.ent.gz	747.8 KB	Display	PDB format
PDBx/mmJSON format	7ri3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7ri3_validation.pdf.gz	481.9 KB	Display	wwPDB validaton report
Full document	7ri3_full_validation.pdf.gz	505.3 KB	Display
Data in XML	7ri3_validation.xml.gz	83.5 KB	Display
Data in CIF	7ri3_validation.cif.gz	115 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ri/7ri3 ftp://data.pdbj.org/pub/pdb/validation_reports/ri/7ri3	HTTPS FTP

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Related structure data

Related structure data	7rb4C 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: Diphtheria_T domain-containing protein

B: Diphtheria_T domain-containing protein

C: Diphtheria_T domain-containing protein

D: Diphtheria_T domain-containing protein

hetero molecules

258 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Diphtheria_T domain-containing protein

hetero molecules

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

2

B: Diphtheria_T domain-containing protein

hetero molecules

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

3

C: Diphtheria_T domain-containing protein

hetero molecules

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

4

D: Diphtheria_T domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	106.950, 137.080, 203.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

#1: Protein	Diphtheria_T domain-containing protein Mass: 64324.578 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albireticuli (bacteria) / Gene: CK936_18545 / Production host: Escherichia coli (E. coli) / Variant (production host): NiCo21(DE3) / References: UniProt: A0A2A2D7J4
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 511 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 2.82 Å³/Da / Density % sol: 56.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10 mM Tris-HCl pH 7.0, 200 mM calcium acetate hydrate, 20% PEG3000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.97951 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 10, 2018
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97951 Å / Relative weight: 1
Reflection	Resolution: 2.687→200 Å / Num. obs: 83962 / % possible obs: 99.9 % / Redundancy: 13.9 % / B_iso Wilson estimate: 49.43 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.189 / R_pim(I) all: 0.052 / R_rim(I) all: 0.196 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.687→2.696 Å / Redundancy: 14.8 % / R_merge(I) obs: 1.435 / Num. unique obs: 803 / CC_1/2: 0.833 / R_pim(I) all: 0.383 / R_rim(I) all: 1.486 / % possible all: 100

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Processing

Software

Name	Version	Classification
autoPROC	1.05	data processing
autoPROC	1.05	data reduction
autoPROC	1.05	data scaling
CRANK2		phasing
PHENIX	1.19.1_4122+SVN	refinement

Refinement

Method to determine structure:

SAD / Resolution: 2.69→60.8 Å / SU ML: 0.357 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2477	4120	4.91 %
R_work	0.2025	79761	-
obs	0.2048	83881	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 52.13 Å²

Refinement step

Cycle: LAST / Resolution: 2.69→60.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17684	0	72	511	18267

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	18201
X-RAY DIFFRACTION	f_angle_d	0.7818	24808
X-RAY DIFFRACTION	f_chiral_restr	0.0481	2782
X-RAY DIFFRACTION	f_plane_restr	0.007	3219
X-RAY DIFFRACTION	f_dihedral_angle_d	12.7594	6716

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 (%)
2.69-2.72	0.3335	151	0.2673	2666	X-RAY DIFFRACTION	99.82
2.72-2.75	0.3472	151	0.28	2749	X-RAY DIFFRACTION	99.83
2.75-2.79	0.3673	146	0.2805	2692	X-RAY DIFFRACTION	100
2.79-2.82	0.3721	132	0.2931	2732	X-RAY DIFFRACTION	99.86
2.82-2.86	0.3387	130	0.3246	2718	X-RAY DIFFRACTION	99.82
2.86-2.9	0.322	130	0.2813	2746	X-RAY DIFFRACTION	99.97
2.9-2.95	0.3422	134	0.2818	2728	X-RAY DIFFRACTION	99.9
2.95-2.99	0.3387	143	0.2707	2727	X-RAY DIFFRACTION	99.83
2.99-3.04	0.3071	147	0.2466	2711	X-RAY DIFFRACTION	99.93
3.04-3.09	0.2964	126	0.2514	2718	X-RAY DIFFRACTION	99.93
3.09-3.15	0.267	136	0.2485	2744	X-RAY DIFFRACTION	99.9
3.15-3.21	0.3205	149	0.2472	2704	X-RAY DIFFRACTION	99.89
3.21-3.28	0.3534	137	0.2438	2748	X-RAY DIFFRACTION	99.93
3.28-3.35	0.2795	127	0.2473	2776	X-RAY DIFFRACTION	99.97
3.35-3.43	0.2903	131	0.2433	2723	X-RAY DIFFRACTION	99.96
3.43-3.51	0.2724	129	0.2411	2741	X-RAY DIFFRACTION	99.9
3.51-3.61	0.2224	144	0.2055	2738	X-RAY DIFFRACTION	99.9
3.61-3.71	0.2681	150	0.1977	2744	X-RAY DIFFRACTION	99.93
3.71-3.83	0.2582	137	0.1824	2761	X-RAY DIFFRACTION	99.9
3.83-3.97	0.213	142	0.1724	2741	X-RAY DIFFRACTION	99.97
3.97-4.13	0.2196	145	0.1689	2735	X-RAY DIFFRACTION	99.97
4.13-4.32	0.2125	153	0.1568	2748	X-RAY DIFFRACTION	99.93
4.32-4.54	0.1987	130	0.1479	2779	X-RAY DIFFRACTION	100
4.54-4.83	0.1756	146	0.1458	2771	X-RAY DIFFRACTION	100
4.83-5.2	0.1861	142	0.1491	2764	X-RAY DIFFRACTION	99.93
5.2-5.72	0.24	169	0.1683	2780	X-RAY DIFFRACTION	99.93
5.72-6.55	0.2391	134	0.1744	2825	X-RAY DIFFRACTION	100
6.55-8.25	0.1819	161	0.1815	2844	X-RAY DIFFRACTION	99.97
8.25-60.8	0.2136	168	0.1917	2908	X-RAY DIFFRACTION	98.18

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	1.820834423	-0.15558780285	0.709308306337	3.89178444689	-0.967770660897	1.84017263358	0.0591654002768	0.229786012878	0.0464474704126	-0.0774001409968	-0.14346319049	-0.264802335387	0.0695342562294	0.543951887222	0.0842975936673	0.220001563561	0.0306983461351	0.00842771746309	0.444935992971	0.0220869608204	0.351757571079	5.52067593784	39.5951403447	-22.8248565858
2	3.19905530372	-1.42343711629	0.376939594169	6.35525188219	-2.38958624098	2.86961174124	0.15184341129	0.167371345896	0.208225350828	-0.0246461975602	-0.141800668966	0.000793603873754	-0.833475920724	-0.172193626933	-0.00944831446314	0.601915620225	0.0711417850816	0.0176765867261	0.382966753199	0.0358185601816	0.286859361467	-19.0495483699	62.5789852969	-50.362433787
3	1.85938756316	-0.359395046836	0.320725009065	2.47135919932	-1.21911782321	2.95261455784	0.0823853801321	0.0110536540577	-0.171723115312	-0.130309853697	-0.0978822040314	-0.202726357357	0.258037601387	0.186826176107	0.0218443576678	0.231271868034	0.0154370034082	-0.00644929465707	0.240854870182	-0.0208131267453	0.296549115137	-18.1136813775	36.2814020245	-29.1375966751
4	1.63535360071	0.817668973611	-0.107952187297	5.60103383599	-1.42895598831	2.30387261909	-0.00552117719695	0.0877058206421	-0.0153472668862	0.0127272557268	-0.257721432521	-0.615177391592	-0.11761191913	0.320451720733	0.249868999425	0.321304035168	0.0847244016994	0.0553780566746	0.392167873419	0.0816589555611	0.38751942182	0.595213672642	30.2973698695	-79.9932780489
5	1.79618071805	1.31556232068	-1.74565688537	3.0072215661	-2.06931745874	3.4088902382	-0.0804786369158	-0.209727909501	-0.186925699906	-0.0459904347377	-0.0605581427205	-0.200543027237	0.21903702405	0.114210582038	0.159047187622	0.348122303253	0.0937481502306	-0.0160482831274	0.305790829485	0.0366661360455	0.309950041299	-23.0453946059	7.03517146415	-53.1594138736
6	2.41627139418	0.487747699919	-0.0802894508177	2.50820370803	-0.972559102207	1.92933506452	0.0296901745767	0.106593634989	0.124255171166	-0.0486166035302	0.00800323155074	-0.0743483096478	-0.316993700597	-0.0817201303011	-0.0438107815979	0.384791754603	0.0665512128031	0.0195801397123	0.248941040245	-0.0302664745427	0.271409883602	-23.9007037945	32.0930757886	-72.3897775916
7	2.77044856605	1.11278605057	-0.49786899546	5.28987226681	-0.590347214525	1.33886662963	0.222451588797	-0.230207029034	0.590631229713	0.619194320985	-0.319999617559	-0.124568049026	-0.439615432391	0.21274113799	0.0936013029963	0.403200936294	-0.0746208899961	-0.0341407336702	0.357819096491	0.0111239513009	0.453761414336	-24.3116295563	-4.09236549452	4.4735615761
8	7.21235462946	-4.31315171535	-1.49296892577	7.26305495376	0.39625852071	4.21061709368	-0.185981735631	-0.312904909335	-0.0256532848392	0.393224049246	0.146546029996	-0.0137041608148	0.184289545011	-0.00519406034789	0.076116807449	0.246553868111	-0.0786660397303	-0.0221132782469	0.256828832448	0.0492173416175	0.290196839642	-35.7649409013	-26.0855550262	-2.68460444897
9	2.00386306869	1.59084555592	0.836049652104	3.02173807045	0.925223632765	2.42214128286	-0.00746147183255	0.131413942203	-0.129898321608	-0.128639512851	0.0211108972494	-0.104916083394	0.024936520204	0.12995519099	-0.0022576868761	0.184103475992	0.0738784892138	0.00892220761814	0.35994730172	0.0622938709873	0.34705928248	-57.2831777762	-27.6027230917	-21.0272957656
10	4.64113295828	4.35804963657	0.957020396493	5.27114433928	1.5005015325	0.545845628448	0.11421875245	-0.176861165333	-0.0164839020243	0.380962390785	-0.198032450955	-0.061734691831	-0.329435186174	-0.108446274677	0.0880590437653	0.255361885232	0.0649335817852	-0.00175833614629	0.425048505745	0.137699145501	0.429189770852	-37.5147755569	0.876917612834	-14.8501382046
11	3.88751386045	2.11641588898	-0.0134956950503	3.95020617805	-0.269447733802	3.00782961812	-0.0222254502809	0.125147087486	0.182797861613	-0.0267576945262	-0.151336028337	-0.363648804479	0.0348279352122	0.468146258987	0.133825518737	0.199732582268	0.0615349746738	-0.00489770108229	0.386153591909	0.132620276404	0.359482363671	-32.4110327181	-6.73890024281	-17.9349312992
12	3.03994004683	4.31029657335	3.3609503994	6.00627496439	3.83617490556	5.59853271762	-0.207504476064	0.381888969166	0.169786247347	-0.0910468074225	0.112028590119	-0.188419209877	-0.0583511133865	0.271500299641	0.0906237184142	0.241445643547	0.0927763858715	0.0841616655361	0.423513603499	0.141498124881	0.439023982876	-32.2647449436	-2.82107979697	-29.535066127
13	0.984335189343	0.854136650837	-0.0592485730411	3.14724594406	-0.0763814441505	1.72942737784	0.0505769044388	-0.156933585105	-0.0595069312104	0.327184291061	-0.108253668264	0.100866713433	0.0994153713192	0.00427993126712	0.062573116058	0.43306056155	-0.0512816263808	0.0100831256646	0.381517652699	-0.0274959621109	0.292549028467	-33.4409301093	9.26994346084	-99.2836896062
14	3.68147526341	1.55554936028	-0.85624751165	5.10635265572	-1.76677604747	4.40760244749	0.0340849963421	-0.234421898619	0.0911189950128	0.0231945822038	-0.0355711018018	0.0414810713539	0.0685825968145	-0.140895223729	-0.00346153809567	0.267716367015	-0.0534825716689	0.0173432703171	0.361052865033	-0.0545530658022	0.283433034914	-2.15551804253	27.3030145363	-122.8437028
15	3.13483491585	1.64750978312	-0.182850961583	3.07680731573	-0.0550888219056	2.15822148007	-0.128577591903	0.0925175818181	-0.37053625774	-0.286625576816	0.00773141515894	-0.00915877857903	0.12332200985	-0.0979332035725	0.112510796154	0.46424310995	-0.0472803230065	0.0353343565399	0.29553228947	-0.0616460946746	0.319336204104	-26.789113304	4.43163701281	-122.613294601

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 6 through 234 )	A	A	6 - 234	1 - 219
2	2	chain 'A' and (resid 235 through 394 )	A	A	235 - 394	220 - 379
3	3	chain 'A' and (resid 395 through 587 )	A	A	395 - 587	380 - 572
4	4	chain 'B' and (resid 5 through 201 )	B	D	5 - 201	1 - 197
5	5	chain 'B' and (resid 202 through 394 )	B	D	202 - 394	198 - 382
6	6	chain 'B' and (resid 395 through 587 )	B	D	395 - 587	383 - 575
7	7	chain 'C' and (resid 5 through 181 )	C	G	5 - 181	1 - 177
8	8	chain 'C' and (resid 182 through 234 )	C	G	182 - 234	178 - 230
9	9	chain 'C' and (resid 235 through 394 )	C	G	235 - 394	231 - 390
10	10	chain 'C' and (resid 395 through 436 )	C	G	395 - 436	391 - 432
11	11	chain 'C' and (resid 437 through 533 )	C	G	437 - 533	433 - 529
12	12	chain 'C' and (resid 534 through 587 )	C	G	534 - 587	530 - 583
13	13	chain 'D' and (resid 6 through 234 )	D	J	6 - 234	1 - 225
14	14	chain 'D' and (resid 235 through 394 )	D	J	235 - 394	226 - 385
15	15	chain 'D' and (resid 395 through 587 )	D	J	395 - 587	386 - 578

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-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

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

-
Data collection

-
Processing

+
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

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Yorodumi