PDB-8qjb: T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core doma...

ID or keywords:

Entry

Database: PDB / ID: 8qjb

Title

T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain extended N-terminus

Components

T6SS-associated Rhs core domain

Keywords

CELL INVASION / Rhs / T6SS / PAAR-Rhs / toxin cannister / Rhs-repeat

Function / homology

Function and homology information

metal ion binding
Similarity search - Function

Biological species

Salmonella bongori N268-08 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.09 Å

Authors

Kielkopf, C.S. / Shneider, M.M. / Leiman, P.G. / Taylor, N.M.I.

Funding support

Switzerland, 1items

Citation

Journal: Structure / Year: 2024
Title: T6SS-associated Rhs toxin-encapsulating shells: Structural and bioinformatical insights into bacterial weaponry and self-protection.
Authors: Kielkopf, C.S. / Shneider, M.M. / Leiman, P.G. / Taylor, N.M.I.

History

Deposition	Sep 13, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 25, 2024	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2	Dec 18, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8qjb.cif.gz	1013.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8qjb.ent.gz	695.1 KB	Display	PDB format
PDBx/mmJSON format	8qjb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/8qjb ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qjb	HTTPS FTP

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Related structure data

Related structure data	8qjaC 8qjcC 8qjdC C: citing same article (ref.)
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

Deposited unit

A: T6SS-associated Rhs core domain

B: T6SS-associated Rhs core domain

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

1

A: T6SS-associated Rhs core domain

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

2

B: T6SS-associated Rhs core domain

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

Unit cell

Length a, b, c (Å)	102.734, 118.733, 130.651
Angle α, β, γ (deg.)	90.000, 105.812, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 360 through 431 or resid 433...
d_2	ens_1	(chain "B" and (resid 360 through 431 or resid 433...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	GLU	GLU	TYR	TYR	A	A	360 - 431	17 - 88
d_1	2	ILE	ILE	SER	SER	A	A	433 - 794	90 - 451
d_1	3	ASN	ASN	ASN	ASN	A	A	796	453
d_1	4	ALA	ALA	THR	THR	A	A	798 - 865	455 - 522
d_1	5	LEU	LEU	LEU	LEU	A	A	867 - 1100	524 - 757
d_1	6	GLY	GLY	GLY	GLY	A	A	1102 - 1219	759 - 876
d_1	7	PRO	PRO	LEU	LEU	A	A	1222 - 1398	879 - 1055
d_1	8	GLY	GLY	LEU	LEU	A	A	1400 - 1420	1057 - 1077
d_2	1	GLU	GLU	TYR	TYR	B	B	360 - 431	17 - 88
d_2	2	ILE	ILE	SER	SER	B	B	433 - 794	90 - 451
d_2	3	ASN	ASN	ASN	ASN	B	B	796	453
d_2	4	ALA	ALA	THR	THR	B	B	798 - 865	455 - 522
d_2	5	LEU	LEU	LEU	LEU	B	B	867 - 1100	524 - 757
d_2	6	GLY	GLY	GLY	GLY	B	B	1102 - 1219	759 - 876
d_2	7	PRO	PRO	LEU	LEU	B	B	1222 - 1398	879 - 1055
d_2	8	GLY	GLY	LEU	LEU	B	B	1400 - 1420	1057 - 1077

#1: Protein	T6SS-associated Rhs core domain Mass: 123894.758 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella bongori N268-08 (bacteria) / Gene: A464_2174 / Production host: Escherichia coli B (bacteria) / Strain (production host): B834 / References: UniProt: S5MXP0
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: 3.15 Å³/Da / Density % sol: 60.94 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop Details: Protein solution (1 ul, 4 mg/ml) was mixed with 1 ul reservoir solution (0.1 M MES pH 6.5, 30% ethylene glycol, 7% PEG 8,000) and 0.2 ul of JBScreen Plus compound B9 (2M sodium fluoride)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9788 Å / Relative weight: 1
Reflection	Resolution: 3.09→47.5 Å / Num. obs: 55140 / % possible obs: 99.44 % / Redundancy: 6.857 % / B_iso Wilson estimate: 51.1 Å² / CC_1/2: 0.997 / CC star: 0.999 / R_merge(I) obs: 0.1216 / R_pim(I) all: 0.05004 / R_rim(I) all: 0.1317 / Net I/σ(I): 15.16
Reflection shell	Resolution: 3.091→3.201 Å / R_merge(I) obs: 0.5997 / Num. unique obs: 5262 / CC_1/2: 0.907 / CC star: 0.975 / R_pim(I) all: 0.2507 / R_rim(I) all: 0.6512

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
PHENIX	1.20.1_4487	refinement
Coot	0.9.3	model building
BUCCANEER		model building
PHASER		phasing
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: Rhs core domain

Resolution: 3.09→47.5 Å / SU ML: 0.3962 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 24.9925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2268	5403	5.02 %
R_work	0.1853	102262	-
obs	0.1874	55106	99.07 %

Solvent computation

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

Displacement parameters

B_iso mean: 60.15 Å²

Refinement step

Cycle: LAST / Resolution: 3.09→47.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16862	0	0	0	16862

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0017	17262
X-RAY DIFFRACTION	f_angle_d	0.4526	23434
X-RAY DIFFRACTION	f_chiral_restr	0.04	2440
X-RAY DIFFRACTION	f_plane_restr	0.0036	3110
X-RAY DIFFRACTION	f_dihedral_angle_d	12.2673	6358

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.423121171425 Å

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 (%)
3.09-3.13	0.4213	143	0.3605	2764	X-RAY DIFFRACTION	81.8
3.13-3.16	0.3796	202	0.3419	3394	X-RAY DIFFRACTION	99.7
3.16-3.2	0.3908	180	0.3016	3496	X-RAY DIFFRACTION	99.54
3.2-3.24	0.3176	176	0.2774	3341	X-RAY DIFFRACTION	99.32
3.24-3.28	0.2994	177	0.2485	3472	X-RAY DIFFRACTION	99.73
3.28-3.33	0.2351	197	0.2265	3470	X-RAY DIFFRACTION	99.76
3.33-3.38	0.2682	178	0.217	3403	X-RAY DIFFRACTION	99.89
3.38-3.43	0.2518	178	0.2172	3414	X-RAY DIFFRACTION	99.47
3.43-3.48	0.267	174	0.2159	3418	X-RAY DIFFRACTION	99.83
3.48-3.54	0.2967	190	0.227	3458	X-RAY DIFFRACTION	99.89
3.54-3.6	0.2895	184	0.2169	3451	X-RAY DIFFRACTION	99.86
3.6-3.66	0.2831	154	0.2008	3472	X-RAY DIFFRACTION	99.89
3.66-3.73	0.2199	201	0.1907	3423	X-RAY DIFFRACTION	99.86
3.73-3.81	0.2325	159	0.1809	3458	X-RAY DIFFRACTION	99.89
3.81-3.89	0.2457	185	0.1855	3375	X-RAY DIFFRACTION	99.8
3.89-3.98	0.1861	205	0.18	3443	X-RAY DIFFRACTION	99.92
3.98-4.08	0.2478	161	0.1717	3494	X-RAY DIFFRACTION	99.7
4.08-4.19	0.2155	183	0.1694	3396	X-RAY DIFFRACTION	99.75
4.19-4.32	0.198	206	0.1564	3440	X-RAY DIFFRACTION	99.84
4.32-4.46	0.1899	166	0.1496	3450	X-RAY DIFFRACTION	99.56
4.46-4.62	0.1479	182	0.1378	3440	X-RAY DIFFRACTION	99.48
4.62-4.8	0.1779	179	0.1299	3395	X-RAY DIFFRACTION	99.53
4.8-5.02	0.1454	177	0.1372	3440	X-RAY DIFFRACTION	99.89
5.02-5.28	0.2239	176	0.1542	3441	X-RAY DIFFRACTION	99.72
5.28-5.61	0.2012	185	0.1583	3427	X-RAY DIFFRACTION	99.64
5.61-6.05	0.2024	185	0.1643	3429	X-RAY DIFFRACTION	99.81
6.05-6.65	0.2207	176	0.1671	3423	X-RAY DIFFRACTION	99.72
6.65-7.61	0.1999	185	0.1954	3433	X-RAY DIFFRACTION	99.83
7.61-9.58	0.2018	181	0.1651	3437	X-RAY DIFFRACTION	99.64
9.58-47.5	0.2037	178	0.1827	3365	X-RAY DIFFRACTION	97.52

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	0.382415872745	-0.718419232978	0.159272471358	2.16957249017	-0.0908983720323	0.565273871312	0.0072451425235	0.0676286529217	0.07349175583	-0.121704760614	0.0395586403465	-0.470238720717	-0.267514012185	0.266150683789	-0.0491195313922	0.580902957441	-0.0686398303295	0.0513128140127	0.464179555209	-0.0336526175075	0.433273445528	23.7035840441	-33.8445727983	-18.2138128661
2	0.873524524775	0.290330160029	0.0703513008877	1.95918843582	0.274272909382	0.458903346889	-0.000139380748471	0.169336978727	0.0202561066828	-0.328297240523	-0.000520952566939	-0.00795816766895	-0.17538163853	0.211696105662	0.000569576799364	0.683831246825	-0.0460750144331	0.0546595740667	0.446949572967	0.00755279450128	0.291765345865	14.2693124692	-27.7695341057	-20.1681895074
3	0.506278147068	0.0324169702546	0.113815502706	1.32453570529	0.107793404174	0.460428110086	-0.0101014383055	0.0159627675777	-0.0196361079147	-0.0762860633416	0.0260835782711	-0.080339185363	0.0537878176588	0.0746883096069	-0.0139338163356	0.545920117428	-0.0273760327578	-0.00895801058636	0.400140824831	0.003182060217	0.236647509357	13.1068332498	-25.034469134	3.88992500088
4	1.34122203386	0.175243232064	0.0763969659345	1.28574799657	-0.0789194806003	0.918288657864	0.081559366572	-0.0718892504678	-0.173466413404	0.521048364802	-0.0395886237397	-0.138429599875	0.122864473131	0.0979445866306	-0.0371339764965	0.739905853397	0.0368521545416	-0.120625113779	0.364224658905	-0.0182973690128	0.333048729302	13.0084486739	-25.6783300334	30.971366288
5	1.92000706648	0.96058155802	-0.104270453358	7.61490118622	-2.31699748613	4.59651479641	0.0683303313803	0.00619077490969	-0.0318367092306	0.290299855452	-0.0407083375762	0.797386701022	-0.136241302118	-0.674559398428	-0.0178735899437	0.474227340035	0.006549068667	0.0458749328289	0.333318115505	-0.00953022246509	0.364584622203	-16.8210541858	-11.2175882289	25.5657045943
6	0.531750953473	-0.113926501568	0.259421194113	1.35518420523	0.205684710617	1.18325155296	-0.108331187016	-0.178735056409	0.00465194939103	0.567211764886	0.0508549878299	0.0565872764612	-0.0728906854576	-0.0343078752381	0.0656914964581	0.775434915815	0.00399236343241	-0.00869256758023	0.406247126427	0.00495975447529	0.317952341958	0.982330393786	-7.34630090612	36.8991138993
7	1.12706318025	-0.698019963338	-0.418678343135	2.2869985382	0.284049932859	0.49713509403	0.0660661471443	0.0921158615664	0.016243020006	-0.0921333519219	-0.0823202431471	-0.319534275516	-0.0306311114148	0.0809245128909	0.0251400990729	0.420348104052	0.00582064940527	-0.0222081701061	0.414391914593	0.0309443490018	0.371335547067	-11.9841589794	-36.9416332664	-79.8708855936
8	0.804019038535	0.546329928028	0.572134510204	1.64830753194	0.161666508621	0.873401123148	-0.0309156081851	0.206754707008	0.0375709212002	-0.299912642491	0.0293945097771	-0.306252454365	-0.1114038758	0.239778336633	0.0175751427947	0.455108247537	-0.00548480929267	0.12050118149	0.449274835805	0.0244207080644	0.399583682475	-9.8675995985	-16.4819355849	-74.1580038586
9	1.95178073842	-0.16463982137	0.377140671496	1.44016691283	0.0800015208958	0.351504332863	0.0104111219372	-0.084123643201	-0.10650228847	0.142020917065	-0.018412955112	-0.0997146202112	0.0635920986299	-0.0083881358308	0.0289557546266	0.489848255091	-0.0616465941959	-0.0448406663482	0.323270145222	0.00135163924439	0.256884501301	-27.130676635	-37.8440770745	-57.0088988148
10	0.56085405926	-0.0065318872978	0.407157258716	1.71218801648	0.0756488088981	0.975217609096	-0.0149194623559	-0.0035294455018	0.0687496864923	0.172659647578	-0.0224570297139	-0.385588042151	-0.0638542046374	0.175148602991	0.021171147428	0.435670892638	-0.0946171728947	-0.0395247974458	0.432294587204	0.0410416620302	0.435902301769	-17.9740859357	-6.47835703765	-46.8882063859
11	0.852165375912	-0.0188322994936	-0.137386961058	1.52733833226	0.296284331633	0.693842374631	0.0584375042741	-0.134219611999	-0.283035214702	0.625813013301	-0.0237923978036	0.0904964583141	0.370941333807	-0.122841306196	-0.0386473513628	0.83461803446	-0.157470223894	-0.00921286484101	0.418168222999	0.0264865469308	0.398702851207	-39.4506430787	-27.9264503894	-32.0968757121
12	4.30027741453	-0.830553211625	0.957738160434	2.38640193544	-0.0109769449519	1.60557106106	-0.0168792554861	-0.483249295712	0.162468443803	0.574948443142	-0.070908636735	0.0813204185984	0.00183447156487	-0.196151081502	0.0970320086507	0.742294450588	-0.110543621285	0.0156246624069	0.366161263236	0.00845714326209	0.288531981741	-40.3729509165	5.02370909176	-28.9469390742
13	1.65550475243	0.0903246390301	-0.0167402375811	0.907626071606	0.451116527157	1.34338641498	0.0682743119103	-0.357455052861	-0.0300600186453	0.763557662921	-0.057829324786	-0.0762193009585	0.196488436881	-0.0959472195182	-0.00362149885671	0.887542984072	-0.103151600699	-0.0608687844403	0.419355005983	0.0222870540507	0.369918944591	-34.6965320084	-14.5280444147	-24.794372728

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 360 through 453 )	A	A	360 - 453	1 - 94
2	2	chain 'A' and (resid 454 through 610 )	A	A	454 - 610	95 - 251
3	3	chain 'A' and (resid 611 through 903 )	A	A	611 - 903	252 - 544
4	4	chain 'A' and (resid 904 through 1080 )	A	A	904 - 1080	545 - 710
5	5	chain 'A' and (resid 1081 through 1139 )	A	A	1081 - 1139	711 - 769
6	6	chain 'A' and (resid 1140 through 1420 )	A	A	1140 - 1420	770 - 1037
7	7	chain 'B' and (resid 360 through 517 )	B	B	360 - 517	1 - 158
8	8	chain 'B' and (resid 518 through 667 )	B	B	518 - 667	159 - 308
9	9	chain 'B' and (resid 668 through 819 )	B	B	668 - 819	309 - 460
10	10	chain 'B' and (resid 820 through 965 )	B	B	820 - 965	461 - 606
11	11	chain 'B' and (resid 966 through 1120 )	B	B	966 - 1120	607 - 750
12	12	chain 'B' and (resid 1121 through 1250 )	B	B	1121 - 1250	751 - 867
13	13	chain 'B' and (resid 1251 through 1420 )	B	B	1251 - 1420	868 - 1037

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