PDB-8cx8: Stx2A1-BTB13086

ID or keywords:

Entry

Database: PDB / ID: 8cx8

Title

Stx2A1-BTB13086

Components

rRNA N-glycosylase

Keywords

TOXIN

Function / homology

Function and homology information

rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.905 Å

Authors

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

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Stx2A1-BTB13086
Authors: Rudolph, M.J. / Li, X.P.

History

Deposition	May 20, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cx8.cif.gz	210.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8cx8.ent.gz	167.5 KB	Display	PDB format
PDBx/mmJSON format	8cx8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cx8_validation.pdf.gz	472.9 KB	Display	wwPDB validaton report
Full document	8cx8_full_validation.pdf.gz	475.6 KB	Display
Data in XML	8cx8_validation.xml.gz	21.3 KB	Display
Data in CIF	8cx8_validation.cif.gz	30.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cx/8cx8 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/8cx8	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: rRNA N-glycosylase

B: rRNA N-glycosylase

hetero molecules

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

1

A: rRNA N-glycosylase

hetero molecules

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

2

B: rRNA N-glycosylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.633, 78.622, 87.337
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 1 through 21 or resid 23...
2	1	(chain B and (resid 1 through 21 or resid 23...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	ARG	ARG	(chain A and (resid 1 through 21 or resid 23...	A	A	1 - 21	2 - 22
1	2	GLU	GLU	THR	THR	(chain A and (resid 1 through 21 or resid 23...	A	A	23 - 36	24 - 37
1	3	VAL	VAL	PHE	PHE	(chain A and (resid 1 through 21 or resid 23...	A	A	38 - 64	39 - 65
1	4	HIS	HIS	ILE	ILE	(chain A and (resid 1 through 21 or resid 23...	A	A	66 - 98	67 - 99
1	5	VAL	VAL	GLN	GLN	(chain A and (resid 1 through 21 or resid 23...	A	A	100 - 175	101 - 176
1	6	GLU	GLU	GLY	GLY	(chain A and (resid 1 through 21 or resid 23...	A	A	177 - 214	178 - 215
1	7	VAL	VAL	ILE	ILE	(chain A and (resid 1 through 21 or resid 23...	A	A	218 - 223	219 - 224
1	8	PHE	PHE	CYS	CYS	(chain A and (resid 1 through 21 or resid 23...	A	A	225 - 241	226 - 242
2	1	ARG	ARG	ARG	ARG	(chain B and (resid 1 through 21 or resid 23...	B	B	1 - 21	2 - 22
2	2	GLU	GLU	THR	THR	(chain B and (resid 1 through 21 or resid 23...	B	B	23 - 36	24 - 37
2	3	VAL	VAL	VAL	VAL	(chain B and (resid 1 through 21 or resid 23...	B	B	38 - 59	39 - 60
2	4	ALA	ALA	PHE	PHE	(chain B and (resid 1 through 21 or resid 23...	B	B	62 - 64	63 - 65
2	5	MET	MET	MET	MET	(chain B and (resid 1 through 21 or resid 23...	B	B	0	1
2	6	VAL	VAL	GLN	GLN	(chain B and (resid 1 through 21 or resid 23...	B	B	100 - 175	101 - 176
2	7	GLU	GLU	ILE	ILE	(chain B and (resid 1 through 21 or resid 23...	B	B	177 - 223	178 - 224
2	8	PHE	PHE	CYS	CYS	(chain B and (resid 1 through 21 or resid 23...	B	B	225 - 241	226 - 242

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Protein , 1 types, 2 molecules AB

#1: Protein	rRNA N-glycosylase Mass: 28087.582 Da / Num. of mol.: 2 Fragment: Ribosomal inactivating protein catalytic subunit, residues 23-272 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5WPX7, rRNA N-glycosylase

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Non-polymers , 5 types, 244 molecules

#2: Chemical	ChemComp-P1U / 5-(4-chlorophenyl)furan-2-carboxylic acid Mass: 222.624 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₇ClO₃
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.19 Å³/Da / Density % sol: 43.94 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 100 mM MES pH 6.5 and magnesium sulfate 1.6 M

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-E / Wavelength: 0.979 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 38250 / % possible obs: 98.6 % / Redundancy: 5.1 % / R_merge(I) obs: 0.122 / R_pim(I) all: 0.06 / R_rim(I) all: 0.136 / Χ²: 1.236 / Net I/σ(I): 6.4 / Num. measured all: 193882

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	4.2	1.251	1844	0.286	0.676	1.429	0.442	96.6
1.93-1.97	4.8	1.225	1859	0.539	0.612	1.374	0.442	98.8
1.97-2.01	4.8	1.039	1889	0.739	0.515	1.164	0.483	98.2
2.01-2.05	5	0.84	1902	0.814	0.407	0.936	0.519	97.9
2.05-2.09	5	0.737	1857	0.837	0.356	0.821	0.555	98.4
2.09-2.14	4.9	0.6	1892	0.839	0.296	0.672	0.607	98.5
2.14-2.19	5	0.508	1890	0.923	0.249	0.568	0.666	98.6
2.19-2.25	5	0.422	1892	0.953	0.207	0.472	0.738	98.6
2.25-2.32	5	0.352	1882	0.965	0.172	0.393	0.775	98.7
2.32-2.39	5	0.312	1914	0.957	0.153	0.349	0.906	98.7
2.39-2.48	4.9	0.265	1900	0.969	0.132	0.297	0.937	99.2
2.48-2.58	4.8	0.228	1923	0.974	0.115	0.256	1.122	99.3
2.58-2.7	4.4	0.186	1861	0.968	0.097	0.211	1.359	97.2
2.7-2.84	5.3	0.167	1932	0.985	0.08	0.186	1.441	99
2.84-3.02	5.9	0.136	1928	0.99	0.062	0.15	1.7	99.8
3.02-3.25	5.8	0.111	1951	0.992	0.052	0.123	2.019	99.5
3.25-3.58	5.5	0.087	1937	0.992	0.042	0.097	2.237	99.4
3.58-4.09	5.2	0.067	1954	0.994	0.034	0.076	2.416	98.8
4.09-5.16	4.7	0.055	1940	0.996	0.028	0.062	2.427	96.9
5.16-50	5.9	0.047	2103	0.997	0.021	0.052	1.906	99.3

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6X6H

6x6h

Resolution: 1.905→45.279 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2052	1950	5.11 %
R_work	0.1775	36216	-
obs	0.1789	38166	97.16 %

Solvent computation

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

Displacement parameters

B_iso max: 118.35 Å² / B_iso mean: 39.5124 Å² / B_iso min: 17.21 Å²

Refinement step

Cycle: final / Resolution: 1.905→45.279 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3747	0	83	224	4054
B_iso mean	-	-	64.3	45.63	-
Num. residues	-	-	-	-	477

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3922
X-RAY DIFFRACTION	f_angle_d	0.747	5336
X-RAY DIFFRACTION	f_chiral_restr	0.052	623
X-RAY DIFFRACTION	f_plane_restr	0.005	678
X-RAY DIFFRACTION	f_dihedral_angle_d	12.22	2308

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2142	X-RAY DIFFRACTION	5.404	TORSIONAL
1	2	B	2142	X-RAY DIFFRACTION	5.404	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.905-1.9522	0.3291	116	0.2821	2042	78
1.9522-2.005	0.26	134	0.2399	2559	98
2.005-2.064	0.2828	131	0.2122	2604	98
2.064-2.1306	0.2427	128	0.1985	2606	98
2.1306-2.2068	0.22	123	0.1894	2581	98
2.2068-2.2951	0.2313	135	0.182	2610	99
2.2951-2.3996	0.2155	125	0.1776	2623	98
2.3996-2.5261	0.213	156	0.1823	2583	99
2.5261-2.6843	0.2063	140	0.1804	2624	99
2.6843-2.8916	0.2157	149	0.1771	2613	98
2.8916-3.1825	0.1988	148	0.1731	2652	100
3.1825-3.6428	0.1991	151	0.1639	2671	99
3.6428-4.5889	0.1391	143	0.1489	2674	98
4.5889-45.279	0.2225	171	0.1832	2774	98

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	8.4446	-4.6293	-3.033	8.2094	3.3319	6.8327	0.0852	-0.0868	-0.8656	-0.1891	0.1648	0.5266	0.2142	-0.0541	-0.1924	0.2534	-0.0803	-0.0551	0.3373	0.085	0.3657	31.1472	-17.5241	-6.0253
2	6.307	1.9897	3.8852	4.4469	2.0682	5.9141	-0.0993	-0.5706	0.4235	0.3016	-0.1123	0.4172	-0.3666	-0.1797	0.2373	0.2463	0.0301	0.0945	0.2606	-0.049	0.3031	0.7562	-1.3065	-12.0188
3	2.3139	0.2194	0.3158	4.2315	1.2461	2.678	-0.0673	-0.1819	-0.3053	0.1759	-0.0272	0.3272	0.0822	-0.1446	0.0467	0.1594	-0.0006	0.0629	0.1774	0.0209	0.3205	3.7185	-16.5383	-15.8126
4	3.8423	-1.3158	1.1703	4.3045	-1.1412	1.8299	0.083	0.303	-0.332	-0.1105	-0.1191	0.1007	0.1163	0.0871	0.0343	0.1585	0.0015	0.0283	0.191	-0.0575	0.2387	10.8925	-17.9141	-25.2681
5	3.9504	0.8333	1.529	2.8719	0.0465	4.3116	-0.1685	0.0295	0.5571	0.0474	-0.0004	0.0123	-0.3787	0.3009	0.2056	0.2472	-0.0089	-0.0058	0.1936	0.0099	0.3369	12.2356	2.5797	-19.5469
6	3.8438	2.2237	-3.0741	8.0001	-2.8196	7.0524	-0.204	-0.3938	0.4021	0.74	0.1659	-0.5774	-0.7563	0.2604	0.101	0.2906	-0.013	-0.0515	0.1809	-0.0828	0.3705	12.7438	3.6667	-10.0431
7	7.7515	3.4819	-3.0292	6.8162	-2.3668	3.3147	0.1441	-0.6029	-0.4141	0.6024	-0.232	-0.6081	0.0098	0.071	0.1046	0.2521	-0.0509	-0.0953	0.3146	0.0512	0.2312	45.1365	-6.8358	-3.5983
8	5.8844	-0.366	-1.5399	5.1237	0.4633	3.6987	0.3225	-0.524	-0.4975	0.6677	-0.2465	0.2493	0.1312	-0.0259	-0.0618	0.2944	-0.0655	-0.103	0.3584	0.0593	0.1864	35.6303	-7.0515	-0.8183
9	2.4768	-3.9146	-0.9415	6.3727	2.1056	2.4853	0.2086	-0.1789	0.2734	-0.0444	-0.2534	-1.4007	0.0844	0.2966	0.0482	0.2313	-0.0347	0.0056	0.4187	0.0936	0.4903	57.9879	0.9261	-13.7452
10	2.104	3.0497	-2.7081	8.1286	-1.6222	5.312	0.0628	0.0444	0.2898	0.095	0.088	0.2391	0.025	-0.1548	-0.1425	0.2128	-0.0438	-0.0122	0.2542	0.0496	0.2694	37.5958	4.235	-9.278
11	5.1274	-0.0673	-0.7151	2.959	0.2138	1.5451	-0.1196	0.7636	0.3856	-0.3804	0.0785	0.0779	-0.1269	-0.0868	0.0161	0.2592	-0.0841	-0.0155	0.3706	0.0829	0.2529	39.4627	5.5602	-19.1984
12	9.2032	1.8532	-2.5907	2.1943	0.2248	5.1182	-0.2577	0.462	-1.3348	-0.0676	0.0825	-0.6164	0.5229	-0.0094	0.1536	0.3096	-0.0549	0.0379	0.2707	-0.0785	0.5013	43.7754	-12.7318	-15.7241
13	5.9088	1.0772	2.3747	6.8997	1.1421	6.336	-0.0491	0.5459	-0.6817	-0.0494	0.206	0.1473	0.0017	-0.5458	-0.0487	0.1799	-0.072	-0.0385	0.2893	-0.0205	0.3727	26.9023	-13.2195	-12.0326
14	3.6925	-0.2658	-3.2687	4.6819	-0.3898	3.0972	-0.0534	-1.2004	-0.8451	0.4942	-0.443	-0.0573	0.7306	0.7599	0.5653	0.368	-0.0246	-0.0353	0.5001	0.1139	0.4222	25.2439	-21.6264	-10.8272

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 226 through 241 )	B	226 - 241
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1 through 38 )	A	1 - 38
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 91 )	A	39 - 91
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 164 )	A	92 - 164
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 165 through 227 )	A	165 - 227
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 228 through 242 )	A	228 - 242
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 27 )	B	1 - 27
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 28 through 55 )	B	28 - 55
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 56 through 66 )	B	56 - 66
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 83 )	B	67 - 83
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 84 through 164 )	B	84 - 164
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 165 through 192 )	B	165 - 192
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 193 through 211 )	B	193 - 211
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 212 through 225 )	B	212 - 225

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