PDB-8s2m: Xenorhabdus bovienii Rhs C-terminal toxin TreX complex with TriX ...

ID or keywords:

Entry

Database: PDB / ID: 8s2m

Title

Xenorhabdus bovienii Rhs C-terminal toxin TreX complex with TriX immunity protein

Components

Complete genome segment 11/17
Immunity Protein TriX

Keywords

TOXIN / ADP-ribosyltransferase

Function / homology

Function and homology information

: / Scabin-like / Domain of unknown function DUF6531 / RHS protein / Domain of unknown function (DUF6531) / RHS protein / RHS repeat / RHS Repeat / YD repeat / Rhs repeat-associated core / :
Similarity search - Domain/homology

Biological species

Xenorhabdus bovienii SS-2004 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.28 Å

Authors

Jurenas, D. / Terradot, L.

Funding support

Belgium, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Thioredoxin 1 moonlights as a chaperone for an interbacterial ADP-ribosyltransferase toxin.
Authors: Dumont, B. / Terradot, L. / Cascales, E. / Van Melderen, L. / Jurenas, D.

History

Deposition	Feb 18, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 4, 2024	Provider: repository / Type: Initial release
Revision 1.1	Dec 11, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8s2m.cif.gz	125.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8s2m.ent.gz	96.5 KB	Display	PDB format
PDBx/mmJSON format	8s2m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8s2m_validation.pdf.gz	430 KB	Display	wwPDB validaton report
Full document	8s2m_full_validation.pdf.gz	431.3 KB	Display
Data in XML	8s2m_validation.xml.gz	16.3 KB	Display
Data in CIF	8s2m_validation.cif.gz	23 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2m ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2m	HTTPS FTP

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Related structure data

Related structure data	8s2nC 9gcoC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Immunity Protein TriX

B: Complete genome segment 11/17

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	77.995, 93.855, 39.903
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2
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	Immunity Protein TriX Mass: 16638.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenorhabdus bovienii SS-2004 (bacteria) Gene: XBJ1_1304 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3UXR2
#2: Protein	Complete genome segment 11/17 Mass: 15317.222 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenorhabdus bovienii SS-2004 (bacteria) Gene: XBJ1_1305 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D3UXR3
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 282 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.37 Å³/Da / Density % sol: 48.1 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.1 M Sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0,5 % v/v Jeffamine ED-2003

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.8266 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8266 Å / Relative weight: 1
Reflection	Resolution: 1.28→46.93 Å / Num. obs: 76705 / % possible obs: 99.8 % / Redundancy: 13.2 % / CC_1/2: 1 / R_merge(I) obs: 0.054 / R_pim(I) all: 0.015 / R_rim(I) all: 0.056 / Χ²: 0.96 / Net I/σ(I): 23 / Num. measured all: 1012505
Reflection shell	Resolution: 1.28→1.31 Å / % possible obs: 97.5 % / Redundancy: 11.7 % / R_merge(I) obs: 1.506 / Num. measured all: 64322 / Num. unique obs: 5484 / CC_1/2: 0.692 / R_pim(I) all: 0.455 / R_rim(I) all: 1.575 / Χ²: 0.91 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
PHENIX	1.20_4459	phasing
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.28→40.21 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1849	2000	2.61 %
R_work	0.1707	-	-
obs	0.1711	76602	99.76 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.28→40.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2070	0	0	282	2352

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	2172
X-RAY DIFFRACTION	f_angle_d	0.85	2944
X-RAY DIFFRACTION	f_dihedral_angle_d	5.436	294
X-RAY DIFFRACTION	f_chiral_restr	0.087	312
X-RAY DIFFRACTION	f_plane_restr	0.01	391

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 (%)
1.28-1.31	0.3744	137	0.34	5105	X-RAY DIFFRACTION	97
1.31-1.34	0.2885	142	0.2746	5281	X-RAY DIFFRACTION	100
1.34-1.38	0.2567	140	0.2557	5260	X-RAY DIFFRACTION	100
1.38-1.43	0.2398	143	0.2481	5299	X-RAY DIFFRACTION	100
1.43-1.48	0.2394	141	0.2004	5265	X-RAY DIFFRACTION	100
1.48-1.54	0.1672	142	0.1637	5302	X-RAY DIFFRACTION	100
1.54-1.61	0.1694	141	0.1518	5265	X-RAY DIFFRACTION	100
1.61-1.69	0.1813	143	0.1565	5334	X-RAY DIFFRACTION	100
1.69-1.8	0.2039	142	0.1697	5311	X-RAY DIFFRACTION	100
1.8-1.94	0.1806	144	0.1633	5323	X-RAY DIFFRACTION	100
1.94-2.13	0.1558	144	0.1519	5366	X-RAY DIFFRACTION	100
2.13-2.44	0.1694	143	0.1626	5386	X-RAY DIFFRACTION	100
2.44-3.08	0.2013	146	0.1706	5443	X-RAY DIFFRACTION	100
3.08-40.21	0.1649	152	0.1593	5662	X-RAY DIFFRACTION	100

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	1.2211	-0.0532	0.1721	1.6086	0.3602	1.3329	-0.0371	-0.0204	0.0411	0.026	-0.0035	-0.0898	-0.1283	0.0928	0.0504	0.1397	0.006	-0.0051	0.1416	0.0068	0.1214	-17.1292	29.5858	6.0801
2	8.7349	-1.9491	0.8602	3.7018	0.1959	3.0167	-0.0719	0.7542	-0.7272	-0.0902	-0.2561	0.415	0.4537	-0.1727	0.1873	0.1769	0.0245	0.0142	0.2131	-0.0526	0.203	-23.2905	22.0944	-4.1327
3	2.0154	-0.2429	1.3039	1.4462	0.3706	1.931	-0.0973	-0.1482	-0.001	0.157	0.094	-0.0668	-0.1895	-0.1064	0.0085	0.1713	0.0107	0.0016	0.1541	0.0032	0.1292	-23.3948	32.612	13.0241
4	1.5414	-0.0233	-0.4434	1.6625	1.1933	4.3747	0.0156	-0.0772	0.0991	0.1132	0.1559	-0.3249	-0.1204	0.2605	-0.1819	0.1491	0.0021	-0.0296	0.1502	-0.016	0.1981	-5.201	29.7186	10.9287
5	4.2561	0.7697	0.7938	2.981	-1.3624	0.945	-0.0616	-0.4976	0.073	0.3442	0.0864	0.1509	-0.1084	-0.0771	-0.0523	0.2039	0.0326	-0.0104	0.1761	-0.0042	0.1264	-17.4415	28.7889	18.0515
6	3.0928	-0.4525	1.174	3.8254	0.1965	2.0097	-0.058	-0.2415	-0.1418	0.3203	0.0773	0.1253	-0.0968	-0.2545	-0.0166	0.1124	0.0095	0.0081	0.1287	0.0054	0.135	-28.3944	33.0114	11.6757
7	4.5522	-3.6857	-1.3325	6.203	2.3761	0.9657	0.2285	0.2111	0.0969	-0.4542	-0.1053	-0.1558	-0.1091	0.0425	-0.1056	0.1507	0.0126	-0.0102	0.1812	-0.0033	0.1483	-29.6281	33.5757	-2.7432
8	3.4281	-0.1847	-0.0805	3.784	-1.2694	2.9827	-0.0634	-0.3576	-0.0051	0.4725	0.1108	0.3041	-0.1245	-0.1383	-0.099	0.1932	0.0085	0.0264	0.2138	0.0073	0.158	-33.412	35.5154	14.3711
9	4.47	-1.9603	-0.8618	3.3916	0.6162	2.1201	0.037	0.0817	0.2169	-0.1023	-0.0314	0.0902	-0.2131	-0.2837	0.0028	0.1633	0.0117	-0.0167	0.1581	0.0113	0.1234	-20.0332	5.5347	-8.6578
10	3.5028	-2.0894	-3.48	4.4306	4.1065	6.7207	0.1649	0.3055	-0.01	-0.3783	-0.19	0.1735	-0.2866	-0.4201	0.0575	0.1776	0.0042	-0.0222	0.1943	0.0135	0.2029	-22.2688	5.0966	-6.6648
11	2.0733	-1.583	-1.0577	5.1618	4.3175	6.6218	-0.0791	-0.1532	0.1065	0.4365	-0.175	0.2823	0.2408	-0.4012	0.2941	0.1478	-0.0112	0.0266	0.1829	-0.0264	0.2205	-24.8239	6.9142	3.6866
12	0.7003	0.8975	0.5668	5.2765	3.339	3.2165	0.0512	-0.0241	-0.0018	-0.2407	-0.2664	0.2879	-0.0479	-0.3722	0.2031	0.1696	-0.0039	-0.0001	0.1893	-0.0095	0.1863	-22.5119	1.892	1.1454
13	0.9282	-1.2844	-0.29	3.7747	1.0972	1.2278	-0.0989	-0.0636	-0.1264	0.1972	0.0397	0.1103	0.172	-0.0039	0.0637	0.1408	-0.0029	0.0039	0.1529	0.0192	0.1476	-14.976	5.923	2.7476
14	0.2457	-0.114	0.1037	1.8928	0.6634	0.5461	-0.0214	-0.0269	0.0225	0.0386	-0.0029	0.011	0.0045	-0.0309	0.0168	0.1239	-0.0005	-0.0043	0.1418	0.0105	0.1233	-12.1054	13.4341	-0.0861
15	4.4311	-1.2222	1.206	2.4182	0.1344	1.5297	-0.1052	0.335	0.3272	-0.1938	0.0919	-0.1954	0.0243	0.1054	0.0535	0.1421	-0.0165	0.0096	0.1604	0.0191	0.1651	-0.8013	23.7388	-1.3003
16	1.465	-0.5664	0.4286	2.2804	0.2653	0.5768	0.0402	0.1449	0.0185	-0.2875	-0.0327	-0.0697	-0.0018	0.0455	-0.0046	0.1433	-0.0019	0.0096	0.1502	0.0078	0.1226	-9.2082	13.8476	-6.9909
17	1.1815	1.6893	0.1939	5.463	1.4661	0.747	0.0443	-0.1595	-0.0723	0.2858	0.0003	-0.1392	0.0847	0.0605	-0.049	0.1196	0.0125	-0.0031	0.1643	0.0065	0.1418	-0.4336	13.7492	4.9455
18	3.4605	-0.0569	-0.1654	2.2118	-0.2275	1.9467	-0.0679	-0.151	-0.1673	0.1687	0.0571	0.0936	0.0896	-0.1012	0.0047	0.1716	0.0237	-0.0002	0.1446	0.0058	0.1251	-26.2085	29.2903	13.2027
19	3.5439	-2.5783	1.5856	3.0044	-1.0777	1.9145	-0.0757	-0.2208	-0.0852	0.4403	0.1196	0.1076	-0.0049	-0.0298	-0.0706	0.2317	0.008	-0.0075	0.185	0.0306	0.1311	-17.0747	20.0474	19.3694
20	2.317	-0.461	-0.8781	3.7587	0.5695	4.0428	-0.0623	-0.2228	-0.1722	0.2117	0.0368	-0.291	0.0356	0.1944	0.0148	0.1688	0.0224	-0.0409	0.1704	0.023	0.1473	-8.1534	18.2404	14.9914

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 52 through 66 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 67 through 73 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 74 through 83 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 84 through 101 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 102 through 110 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 111 through 120 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 121 through 129 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 130 through 136 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 3 through 15 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 16 through 27 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 28 through 38 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 39 through 50 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 51 through 61 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 62 through 92 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 93 through 101 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 102 through 119 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 120 through 134 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 9 through 27 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 28 through 37 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 38 through 51 )

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