PDB-8sz2: Stx2A1 bound to P8 stalk peptide

ID or keywords:

Entry

Database: PDB / ID: 8sz2

Title

Stx2A1 bound to P8 stalk peptide

Components

P stalk peptide P8
Shiga-like toxin 2 subunit A

Keywords

TOXIN / Hydrolase / Shiga toxin catalytic subunit / P stalk peptide

Function / homology

Function and homology information

modulation of host virulence by virus / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region
Similarity search - Function

Biological species

Escherichia coli O104:H4 (bacteria)

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.01 Å

Authors

rudolph, M.J. / Li, X.P.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Structure of Shiga toxin 2 A1 subunit with peptides that bind at the ribosome binding site and inhibit activity
Authors: Rudolph, M.J. / Li, X.P.

History

Deposition	May 26, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 29, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sz2.cif.gz	214 KB	Display	PDBx/mmCIF format
PDB format	pdb8sz2.ent.gz	171.6 KB	Display	PDB format
PDBx/mmJSON format	8sz2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sz2_validation.pdf.gz	979.1 KB	Display	wwPDB validaton report
Full document	8sz2_full_validation.pdf.gz	984.6 KB	Display
Data in XML	8sz2_validation.xml.gz	21.6 KB	Display
Data in CIF	8sz2_validation.cif.gz	30.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sz/8sz2 ftp://data.pdbj.org/pub/pdb/validation_reports/sz/8sz2	HTTPS FTP

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Related structure data

Related structure data	6x6hS 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	#161 - May 2013 Ricin similarity (8) #69 - Sep 2005 Cholera Toxin similarity (8)

Deposited unit

A: Shiga-like toxin 2 subunit A

B: Shiga-like toxin 2 subunit A

P: P stalk peptide P8

Q: P stalk peptide P8

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	102.349, 102.349, 92.891
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

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Protein / Protein/peptide , 2 types, 4 molecules ABPQ

#1: Protein	Shiga-like toxin 2 subunit A / SLT-2 A subunit / SLT-2a / SLT-IIa / Verocytotoxin 2 subunit A / Verotoxin 2 subunit A / rRNA N-glycosidase 2 Mass: 27995.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O104:H4 (bacteria) / Gene: stxA2, stx2A, L0103 / Production host: Escherichia coli (E. coli) / References: UniProt: P09385, rRNA N-glycosylase
#2: Protein/peptide	P stalk peptide P8 Mass: 654.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

#1: Protein

Shiga-like toxin 2 subunit A / SLT-2 A subunit / SLT-2a / SLT-IIa / Verocytotoxin 2 subunit A / Verotoxin 2 subunit A / rRNA N-glycosidase 2

Mass: 27995.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli O104:H4 (bacteria) / Gene: stxA2, stx2A, L0103 / Production host:

Escherichia coli (E. coli) / References: UniProt: P09385, rRNA N-glycosylase

#2: Protein/peptide

P stalk peptide P8

Mass: 654.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.)

Escherichia coli (E. coli)

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Non-polymers , 5 types, 194 molecules

#3: Chemical	ChemComp-2PE / NONAETHYLENE GLYCOL Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₃₈O₁₀ / Comment: precipitant*YM
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 49.96 %
Crystal grow	Temperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.9 / Details: 400 mM NaH2PO4 pH 4.9 and 30% PEG 400

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS-II

/ Beamline: 19-ID / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 3, 2023

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.01→50 Å / Num. obs: 36452 / % possible obs: 100 % / Redundancy: 19.2 % / CC_1/2: 0.996 / CC star: 0.999 / R_merge(I) obs: 0.212 / R_pim(I) all: 0.049 / R_rim(I) all: 0.218 / Χ²: 1.12 / Net I/σ(I): 4.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.01-2.07	18.5	2.996	1828	0.487	0.809	0.7	3.077	0.707	100
2.07-2.1	18.3	2.358	1810	0.567	0.851	0.554	2.423	0.723	100
2.1-2.14	18.2	2.085	1808	0.647	0.886	0.494	2.143	0.745	100
2.14-2.19	17.8	1.791	1816	0.762	0.93	0.43	1.842	0.764	100
2.19-2.23	16.6	1.47	1790	0.741	0.923	0.372	1.516	0.787	100
2.23-2.29	16.8	1.303	1834	0.802	0.943	0.326	1.343	0.818	100
2.29-2.34	18.2	1.053	1809	0.895	0.972	0.252	1.083	0.828	100
2.34-2.41	18	0.911	1811	0.913	0.977	0.219	0.937	0.86	100
2.41-2.48	20.1	0.741	1813	0.951	0.987	0.167	0.76	0.868	100
2.48-2.56	20.5	0.607	1812	0.964	0.991	0.136	0.622	0.927	100
2.56-2.65	20.5	0.503	1839	0.979	0.995	0.113	0.515	0.948	100
2.65-2.76	20.5	0.41	1807	0.983	0.996	0.092	0.421	1.018	100
2.76-2.88	20.5	0.331	1828	0.991	0.998	0.074	0.339	1.078	100
2.88-3.03	20.5	0.253	1816	0.993	0.998	0.057	0.26	1.123	100
3.03-3.22	20.5	0.189	1831	0.995	0.999	0.042	0.194	1.247	100
3.22-3.47	20.2	0.144	1819	0.997	0.999	0.033	0.147	1.477	100
3.47-3.82	19.3	0.111	1824	0.997	0.999	0.026	0.114	1.782	100
3.82-4.37	17.3	0.081	1832	0.998	1	0.02	0.083	2.08	100
4.37-5.51	20.4	0.067	1843	0.998	1	0.015	0.068	1.962	100
5.51-50	21.8	0.05	1882	0.999	1	0.011	0.051	1.436	99.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6X6H

6x6h

Resolution: 2.01→23.22 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2114	1790	4.92 %
R_work	0.1729	-	-
obs	0.1749	36390	99.47 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.01→23.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3840	0	65	181	4086

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4008
X-RAY DIFFRACTION	f_angle_d	0.788	5429
X-RAY DIFFRACTION	f_dihedral_angle_d	12.74	1440
X-RAY DIFFRACTION	f_chiral_restr	0.055	633
X-RAY DIFFRACTION	f_plane_restr	0.008	692

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 (%)
2.01-2.07	0.3728	88	0.273	2518	X-RAY DIFFRACTION	94
2.07-2.13	0.2901	133	0.2348	2678	X-RAY DIFFRACTION	100
2.13-2.2	0.2752	146	0.2224	2651	X-RAY DIFFRACTION	100
2.2-2.28	0.2531	112	0.2122	2720	X-RAY DIFFRACTION	100
2.28-2.37	0.2489	144	0.199	2627	X-RAY DIFFRACTION	100
2.37-2.47	0.2613	165	0.1882	2652	X-RAY DIFFRACTION	100
2.48-2.61	0.2375	116	0.1781	2700	X-RAY DIFFRACTION	100
2.61-2.77	0.2091	132	0.1808	2673	X-RAY DIFFRACTION	100
2.77-2.98	0.2188	133	0.1782	2674	X-RAY DIFFRACTION	100
2.98-3.28	0.2156	155	0.1743	2658	X-RAY DIFFRACTION	100
3.28-3.75	0.2195	151	0.156	2668	X-RAY DIFFRACTION	100
3.75-4.72	0.1669	144	0.1347	2682	X-RAY DIFFRACTION	100
4.72-23.22	0.1795	171	0.1686	2699	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	3.2908	-0.4319	-0.3341	0.4319	0.2989	1.9	0.0228	-0.0071	0.4016	0.0787	0.0238	-0.1258	-0.0689	-0.0079	-0.0592	0.2297	-0.0294	-0.0277	0.1821	0.0147	0.2786	16.8671	41.434	-0.5446
2	3.8983	0.0529	-1.9681	3.1661	0.1145	8.9956	0.1247	-0.052	0.3457	0.1184	-0.2065	0.156	-0.9776	-1.0915	-0.0971	0.2526	0.0807	-0.0318	0.253	-0.0377	0.3919	2.9002	46.0291	0.9799
3	3.7265	0.3331	-1.6749	3.5427	1.0998	5.5883	0.17	-0.0045	-0.0021	0.2816	-0.0297	-0.6881	-0.1601	0.7268	-0.1522	0.2314	-0.0494	-0.038	0.2588	-0.0176	0.3239	25.8735	35.657	-7.6439
4	2.4587	0.6223	0.8759	2.6347	-0.5917	3.141	0.0298	0.263	-0.0933	-0.1034	0.1365	0.1546	0.2308	0.0267	-0.1809	0.1913	0.0295	-0.0186	0.2236	-0.0134	0.2148	15.0719	29.8051	-15.8139
5	7.4231	-1.9956	-0.7994	4.3309	-0.0233	2.0574	-0.0096	-0.5659	-0.3168	0.3413	0.0894	-0.0294	0.1687	0.0602	-0.0116	0.3432	-0.0353	-0.0498	0.2416	0.0449	0.2286	13.9856	28.3041	2.791
6	8.3107	-2.0659	-0.6097	6.2277	-0.1374	4.0156	-0.0034	-0.4707	0.0931	0.5978	0.1814	0.5912	-0.0828	-0.5711	-0.0819	0.2581	-0.0585	-0.0033	0.3902	0.0443	0.2776	-4.2265	33.9788	2.1479
7	7.1466	2.6951	0.0434	6.7079	0.5928	7.145	0.0598	-0.4514	-0.2023	0.5303	0.0494	0.1942	0.0347	-0.6712	-0.1717	0.182	0.0093	-0.0056	0.3218	0.0128	0.2529	-1.3195	34.8237	4.9881
8	5.85	2.3142	0.81	5.9815	-1.1402	4.9071	0.2762	-0.3455	0.2162	0.024	-0.1829	0.4098	0.0226	-0.3555	-0.1264	0.2021	0.0064	-0.0028	0.2067	-0.0092	0.1979	-27.5531	34.9058	-17.304
9	4.1472	-1.2283	-2.0946	4.7973	1.0984	8.3926	0.2485	0.3463	0.4552	-0.4629	0.0792	-0.2135	-0.5649	0.3987	-0.3883	0.2313	-0.0138	0.0251	0.2424	0.0393	0.3222	-15.5996	43.5343	-18.7015
10	3.7234	0.6994	0.2906	3.9366	-0.0082	4.0478	0.1064	-0.14	-0.0176	-0.1175	0.1035	0.6382	0.1796	-0.6643	-0.2251	0.1967	-0.0404	-0.0383	0.2857	0.0573	0.3014	-30.0724	29.2774	-8.5522
11	3.0866	-0.2297	0.6847	2.6104	-0.5556	3.3423	0.1907	-0.3426	-0.3458	0.0372	0.1039	0.2255	0.3674	-0.2208	-0.261	0.282	-0.0865	-0.0639	0.2665	0.0571	0.2777	-22.1399	22.1941	-2.502
12	4.394	0.6945	-0.0999	3.7448	-0.5301	4.3222	0.2296	0.4664	-0.0913	-0.3652	-0.0401	-0.1771	0.4631	0.325	-0.0671	0.2997	0.0695	-0.0153	0.2265	-0.0317	0.1649	-12.2824	29.4184	-20.7084
13	6.6223	-0.6597	-1.6803	3.5326	-0.1112	8.6336	0.0234	0.4465	-0.1827	-0.273	-0.2234	-0.247	0.1814	0.4402	-0.0832	0.2577	0.0287	0.0337	0.354	0.0255	0.234	-8.2033	34.3912	-23.3047
14	3.5147	-3.8768	-3.5786	7.5157	3.9644	3.6458	0.5039	0.3239	-0.2063	-0.5619	0.1202	-1.0389	-0.4932	0.5752	-0.6626	0.3854	-0.0607	-0.0038	0.3752	0.0222	0.495	12.9664	38.1025	11.948
15	5.4286	4.554	0.9239	3.8558	0.4925	2.4148	0.1412	-0.2201	0.3676	-0.3279	-0.0307	0.9587	-0.5901	-0.0208	-0.1073	0.4183	0.0325	-0.0571	0.359	-0.002	0.4608	-22.8373	33.3968	-30.272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 164 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 192 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 193 through 220 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 221 through 241 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 0 through 27 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 48 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 76 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 77 through 164 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 165 through 220 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 221 through 241 )
14	X-RAY DIFFRACTION	14	chain 'P' and (resid 6 through 11 )
15	X-RAY DIFFRACTION	15	chain 'Q' and (resid 6 through 11 )

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