PDB-9biw: Crystal structure of Chelona Toxin, a diphtheria toxin homolog, f...

ID or keywords:

Entry

Database: PDB / ID: 9biw

Title

Crystal structure of Chelona Toxin, a diphtheria toxin homolog, from Austwickia chelonae

Components

Chelona Toxin

Keywords

TOXIN / diphtheria toxin / bacterial toxin / ADP-ribosyltransferase / protein delivery

Biological species

Austwickia chelonae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.496 Å

Authors

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

Funding support

Canada, 2items

Citation

Journal: Embo Mol Med
Title: A diphtheria toxin-like intracellular delivery platform that evades pre-existing antidrug antibodies
Authors: Gill, S.K. / Sugiman-Marangos, S.N. / Beilhartz, G. / Mei, E. / Taipale, M. / Melnyk, R.A.

History

Deposition	Apr 24, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9biw.cif.gz	404.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9biw.ent.gz	332 KB	Display	PDB format
PDBx/mmJSON format	9biw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9biw_validation.pdf.gz	440.2 KB	Display	wwPDB validaton report
Full document	9biw_full_validation.pdf.gz	448.2 KB	Display
Data in XML	9biw_validation.xml.gz	40.9 KB	Display
Data in CIF	9biw_validation.cif.gz	58.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bi/9biw ftp://data.pdbj.org/pub/pdb/validation_reports/bi/9biw	HTTPS FTP

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Chelona Toxin

B: Chelona Toxin

hetero molecules

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

1

A: Chelona Toxin

hetero molecules

B: Chelona Toxin

hetero molecules

defined by author&software
116 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.236, 138.835, 152.109
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Chelona Toxin Mass: 57915.387 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Austwickia chelonae (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.2 Å³/Da / Density % sol: 44.05 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2M calcium chloride, 0.1M Tris-HCl pH 341 8.5, 25% (w/v) PEG4000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.496→102.543 Å / Num. obs: 36410 / % possible obs: 100 % / Redundancy: 10.5 % / R_merge(I) obs: 0.233 / Net I/σ(I): 7.1
Reflection shell	Resolution: 2.5→51.27 Å / R_merge(I) obs: 1.146 / Num. unique obs: 2613

-
Processing

Software

Name	Version	Classification
PHENIX	1.16_3549: ???	refinement
autoPROC		data reduction
autoPROC		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.496→51.272 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.53 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2676	1799	4.94 %
R_work	0.2362	-	-
obs	0.2378	36410	99.81 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.496→51.272 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7802	0	7	409	8218

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	7946
X-RAY DIFFRACTION	f_angle_d	0.712	10788
X-RAY DIFFRACTION	f_dihedral_angle_d	15.446	4800
X-RAY DIFFRACTION	f_chiral_restr	0.045	1263
X-RAY DIFFRACTION	f_plane_restr	0.003	1395

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 (%)
2.496-2.5635	0.3544	142	0.3233	2613	X-RAY DIFFRACTION	100
2.5635-2.6389	0.3707	143	0.3023	2606	X-RAY DIFFRACTION	100
2.6389-2.7241	0.316	129	0.2939	2621	X-RAY DIFFRACTION	100
2.7241-2.8214	0.2937	139	0.2675	2656	X-RAY DIFFRACTION	100
2.8214-2.9344	0.2741	108	0.2625	2618	X-RAY DIFFRACTION	100
2.9344-3.0679	0.2731	135	0.2645	2649	X-RAY DIFFRACTION	100
3.0679-3.2297	0.3017	152	0.2667	2632	X-RAY DIFFRACTION	100
3.2297-3.432	0.2953	144	0.2526	2634	X-RAY DIFFRACTION	100
3.432-3.6969	0.246	136	0.2273	2660	X-RAY DIFFRACTION	100
3.6969-4.0688	0.2393	137	0.212	2673	X-RAY DIFFRACTION	100
4.0688-4.6572	0.217	151	0.1873	2661	X-RAY DIFFRACTION	100
4.6572-5.8662	0.2493	140	0.1993	2737	X-RAY DIFFRACTION	100
5.8662-51.272	0.2391	143	0.2098	2851	X-RAY DIFFRACTION	99

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	1.247	-0.7734	-0.145	1.5914	-0.0408	3.2852	0.1077	0.0906	-0.0327	-0.2222	-0.0475	-0.0644	-0.0617	0.0458	-0.1026	0.172	-0.0365	-0.0298	0.1908	-0.037	0.2441	8.1666	-14.6384	-56.9456
2	0.0368	-0.1349	-0.677	0.4883	0.6397	4.0158	0.0498	-0.0146	-0.0233	-0.0195	0.0444	-0.1687	-0.0485	0.05	-0.1109	0.2285	-0.0022	-0.0276	0.2425	-0.0034	0.3879	13.2349	-13.6468	-45.0095
3	0.4639	0.1369	0.027	1.1465	-0.281	1.5365	0.0038	0.0146	-0.0695	0.2311	-0.0358	-0.0159	-0.1419	0.0667	0.0325	0.2228	-0.013	-0.0454	0.2062	-0.0128	0.2688	2.3004	1.4049	-18.9755
4	2.202	-1.098	-0.3844	1.8829	-0.1666	2.585	0.1545	0.0729	-0.0739	-0.1225	-0.0053	0.084	-0.0293	-0.1846	-0.1439	0.1797	-0.0107	-0.0472	0.1765	-0.018	0.2983	-4.8112	3.3499	-47.9531
5	0.8537	-0.7458	-0.727	1.8157	-0.171	2.4203	0.0233	0.0994	0.0065	-0.1642	-0.0354	0.248	0.0592	-0.1878	0.0399	0.1849	0.0169	-0.1016	0.2856	0.0289	0.3099	16.0298	43.8492	-53.2002
6	0.2624	0.3461	0.6473	2.1082	-1.2732	4.442	0.0258	0.0878	0.1383	-0.2821	-0.2085	0.0389	0.3817	-0.0722	-0.0125	0.2677	0.0346	-0.063	0.2398	-0.0094	0.3903	15.3672	45.0437	-47.2167
7	1.7383	0.1584	-0.5035	1.1543	-0.3568	3.027	0.0539	0.2934	-0.3095	-0.78	-0.3016	0.1458	0.3006	0.2379	0.23	0.6232	0.1526	-0.0814	0.4745	-0.0845	0.3334	14.4244	38.9778	-66.7909
8	0.5687	0.7246	-0.4061	0.996	-0.4214	2.9816	0.1433	-0.039	-0.0765	0.1337	-0.1056	-0.0041	0.2815	0.1206	-0.0714	0.2343	0.0399	-0.037	0.2312	-0.0338	0.3257	15.7422	38.318	-27.7023
9	1.3321	0.0319	-0.7492	1.9798	-0.058	1.3708	-0.0911	-0.2034	-0.166	0.1872	-0.0286	-0.0253	0.2049	0.1481	0.0717	0.2292	-0.0194	-0.095	0.1961	0.0201	0.2559	22.9761	23.8231	-17.0987
10	0.5611	-0.5099	-0.478	1.1834	0.7466	1.7464	-0.0767	-0.0785	-0.1919	0.0943	-0.0081	0.0196	0.0488	0.0492	0.0561	0.2457	-0.038	-0.0743	0.2533	0.0418	0.3184	20.0059	26.9432	-25.2765
11	2.315	-0.1848	-0.3513	1.6795	-0.3177	2.7841	0.1416	0.4138	0.0042	-0.2764	-0.1051	0.135	0.3174	0.1023	0.0886	0.2812	0.0717	-0.0782	0.347	0.0088	0.3149	27.0305	22.7912	-50.609
12	1.9796	-1.2402	-0.0109	1.7211	0.5722	2.677	0.1329	0.0891	0.1084	-0.2126	-0.0933	-0.3223	0.0201	0.2043	-0.0533	0.195	0.0392	-0.0075	0.2185	-0.002	0.2748	27.7962	28.4602	-47.8569
13	2.0805	0.1138	-1.0725	3.0298	0.5582	3.0624	0.3943	0.0181	0.2227	-0.1314	0.015	-0.0863	0.1208	0.1445	-0.3235	0.1922	0.0679	-0.0331	0.3145	0.0396	0.3667	34.1497	19.2075	-43.533

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 128 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 129 through 209 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 210 through 400 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 401 through 539 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 5 through 66 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 67 through 93 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 94 through 148 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 149 through 245 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 246 through 317 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 318 through 400 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 401 through 444 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 445 through 510 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 511 through 540 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

Thousand views of thousand structures

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
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

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Links

-Assembly

-Components

-Experimental details

-Experiment

-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

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
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

-
Yorodumi