PDB-9bon: Crystal structure of glucosyltransferase (GTD) domain of TpeL

ID or keywords:

Entry

Database: PDB / ID: 9bon

Title

Crystal structure of glucosyltransferase (GTD) domain of TpeL

Components

TpeL

Keywords

TOXIN / glucosyltransferase / bacterial toxin / targets small GTPases

Function / homology

Function and homology information

host cell cytosol / glycosyltransferase activity / peptidase activity / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.222 Å

Authors

Gill, S. / Sugiman-Marangos, S.N. / Beilhartz, G.L. / Mei, E. / Taipale, M. / Melnyk, R.A.

Funding support

Canada, 2items

Citation

Journal: Embo Mol Med / Year: 2024
Title: A diphtheria toxin-like intracellular delivery platform that evades pre-existing antidrug antibodies.
Authors: Gill, S. / Sugiman-Marangos, S.N. / Beilhartz, G.L. / Mei, E. / Taipale, M. / Melnyk, R.A.

History

Deposition	May 5, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 7, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9bon.cif.gz	451.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9bon.ent.gz	372.4 KB	Display	PDB format
PDBx/mmJSON format	9bon.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9bon_validation.pdf.gz	433.7 KB	Display	wwPDB validaton report
Full document	9bon_full_validation.pdf.gz	443 KB	Display
Data in XML	9bon_validation.xml.gz	40.8 KB	Display
Data in CIF	9bon_validation.cif.gz	57.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/9bon ftp://data.pdbj.org/pub/pdb/validation_reports/bo/9bon	HTTPS FTP

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Related structure data

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	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: TpeL

B: TpeL

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

1

A: TpeL

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

2

B: TpeL

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

Unit cell

Length a, b, c (Å)	75.093, 64.730, 121.181
Angle α, β, γ (deg.)	90.00, 102.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	TpeL Mass: 64790.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: first 545 amino acids of TpeL containing the GTD, with C-terminal 6XHis tag Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: tpeL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A2PYQ6
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.67 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2M potassium sodium tartrate and 20% (w/v) PEG 3350

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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: Dec 14, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 2.22→118.52 Å / Num. obs: 56042 / % possible obs: 99.4 % / Redundancy: 4.6 % / CC_1/2: 0.997 / R_merge(I) obs: 0.08 / R_pim(I) all: 0.042 / R_rim(I) all: 0.09 / Net I/σ(I): 11.2
Reflection shell	Resolution: 2.22→10.31 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2780 / CC_1/2: 0.997 / % possible all: 99.4

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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: 2.222→73.445 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2374	2774	4.95 %
R_work	0.1929	-	-
obs	0.1951	56042	99.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.222→73.445 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8833	0	0	363	9196

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	8980
X-RAY DIFFRACTION	f_angle_d	1.008	12091
X-RAY DIFFRACTION	f_dihedral_angle_d	7.28	5517
X-RAY DIFFRACTION	f_chiral_restr	0.052	1348
X-RAY DIFFRACTION	f_plane_restr	0.006	1530

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 (%)
2.222-2.2603	0.3364	143	0.2958	2637	X-RAY DIFFRACTION	100
2.2603-2.3014	0.3254	151	0.2787	2662	X-RAY DIFFRACTION	99
2.3014-2.3457	0.3244	129	0.2732	2606	X-RAY DIFFRACTION	99
2.3457-2.3936	0.3452	143	0.2642	2649	X-RAY DIFFRACTION	99
2.3936-2.4456	0.3193	143	0.256	2618	X-RAY DIFFRACTION	99
2.4456-2.5025	0.3147	135	0.2528	2677	X-RAY DIFFRACTION	99
2.5025-2.5651	0.3081	137	0.2504	2635	X-RAY DIFFRACTION	99
2.5651-2.6345	0.2968	135	0.2413	2636	X-RAY DIFFRACTION	99
2.6345-2.712	0.2692	142	0.2404	2656	X-RAY DIFFRACTION	100
2.712-2.7995	0.2808	150	0.233	2662	X-RAY DIFFRACTION	100
2.7995-2.8996	0.2897	128	0.2355	2660	X-RAY DIFFRACTION	100
2.8996-3.0157	0.2922	138	0.2368	2689	X-RAY DIFFRACTION	100
3.0157-3.1529	0.3077	127	0.23	2641	X-RAY DIFFRACTION	100
3.1529-3.3192	0.282	132	0.2101	2689	X-RAY DIFFRACTION	99
3.3192-3.5271	0.2631	145	0.1921	2644	X-RAY DIFFRACTION	99
3.5271-3.7994	0.1969	130	0.1682	2691	X-RAY DIFFRACTION	99
3.7994-4.1817	0.176	137	0.1443	2675	X-RAY DIFFRACTION	99
4.1817-4.7868	0.1751	152	0.1356	2671	X-RAY DIFFRACTION	99
4.7868-6.0304	0.1816	129	0.1579	2719	X-RAY DIFFRACTION	100
6.0304-73.445	0.1653	148	0.1524	2751	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	1.8431	-1.2309	0.8771	1.0765	-0.8486	1.2041	-0.0013	-0.2053	-0.288	0.0018	0.0875	0.1415	0.1863	-0.1536	-0.1129	0.3603	-0.0305	0.0043	0.2595	0.0315	0.3961	35.176	-29.203	27.87
2	0.6201	0.1744	0.4214	0.8023	0.1054	1.3617	0.0001	-0.0756	0.0177	0.0359	-0.0313	0.072	-0.078	-0.3627	0.0302	0.2409	0.0233	0.013	0.3521	0.0032	0.3172	17.74	-1.797	8.677
3	3.3439	-0.3783	0.3997	3.7079	-0.2949	3.8388	0.2409	0.2646	0.006	-0.2473	-0.2332	-0.3133	0.0254	0.0982	-0.0472	0.2686	0.0288	0.02	0.2388	0.0385	0.3137	37.005	7.729	21.108
4	1.5686	0.0928	1.4625	1.0137	-0.3106	1.7015	0.0308	0.1657	-0.1746	-0.0197	0.0876	-0.1939	0.0984	0.1831	-0.092	0.2617	-0.0002	0.0289	0.2369	0.0174	0.3614	32.001	-14.382	15.338
5	1.5113	1.3628	0.3898	1.6874	0.7713	0.4595	-0.028	0.2642	-0.0802	0.4678	0.2035	-0.2482	0.027	-0.0588	-0.1484	0.5044	0.079	-0.0258	0.4992	-0.0061	0.3996	29.346	14.184	-2.676
6	3.0083	0.0516	1.1724	1.9879	0.3559	2.6951	-0.0825	-0.0321	0.5656	-0.1869	-0.0549	0.0293	-0.2292	0.1493	0.1088	0.4186	-0.0879	-0.0204	0.2744	0.0079	0.3724	-12.62	-24.413	19.836
7	1.398	-0.0322	-0.0751	1.225	0.8004	2.5663	-0.0763	-0.192	0.004	0.1918	0.0347	-0.0119	0.0236	0.1887	0.0557	0.2871	0.0034	-0.0305	0.282	0.0165	0.2849	6.869	-31.991	63.04
8	0.9958	0.2198	0.8987	0.5893	-0.3988	3.3762	-0.1206	0.1454	0.0678	0.0137	0.1085	-0.0772	-0.394	0.2576	0.0232	0.3464	-0.0208	0.0073	0.3578	-0.0439	0.323	14.932	-23.458	64.221
9	1.8189	-0.7728	0.2599	2.4207	-0.0593	1.747	-0.0234	0.011	-0.4633	0.0687	0.0376	0.1964	0.3709	-0.1533	-0.0164	0.3123	-0.0311	0.0269	0.3399	-0.0338	0.3631	7.613	-50.434	47.928
10	2.0088	-0.2733	-2.2836	0.4818	0.6198	5.5351	0.0644	0.17	0.1982	0.0754	-0.0456	0.2337	-0.6262	-0.8907	-0.078	0.4115	0.0821	-0.0105	0.4421	-0.0097	0.4091	-8.994	-20.571	57.345
11	2.2968	-1.18	0.3078	1.7237	0.0008	2.4523	-0.0792	0.234	-0.2005	0.0873	-0.0348	0.4066	-0.0242	-0.373	0.0785	0.3053	-0.0218	-0.0057	0.3288	-0.0158	0.3239	-6.522	-32.41	41.238
12	1.1684	-1.2046	-1.5521	1.1055	1.546	2.0514	-0.0778	-0.1822	-0.1474	0.5133	-0.0897	0.4545	0.2914	0.0384	0.1998	0.6405	-0.0632	0.1301	0.5266	0.0452	0.6812	-2.486	-42.976	68.381

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:110 )	A	1 - 110
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 111:420 )	A	111 - 420
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 421:462 )	A	421 - 462
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 463:511 )	A	463 - 511
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 512:548 )	A	512 - 548
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 1:89 )	B	1 - 89
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 90:192 )	B	90 - 192
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 193:264 )	B	193 - 264
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 265:393 )	B	265 - 393
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 394:463 )	B	394 - 463
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 464:506 )	B	464 - 506
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 507:536 )	B	507 - 536

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