PDB-8qjd: T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain

ID or keywords:

Entry

Database: PDB / ID: 8qjd

Title

T6SS-linked Rhs repeat protein - Salmonella bongori Rhs-core domain

Components

Salmonella bongori Rhs core domain (residues 360-1420)

Keywords

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

Function / homology

Function and homology information

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

Biological species

Salmonella bongori N268-08 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.203 Å

Authors

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

Funding support

Switzerland, 1items

Citation

Journal: To Be Published
Title: T6SS-associated Rhs proteins form toxin containers: Structural and functional insights into bacterial weaponry and self-protection
Authors: Kielkopf, C.S. / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8qjd.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8qjd.ent.gz	712.6 KB	Display	PDB format
PDBx/mmJSON format	8qjd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8qjd_validation.pdf.gz	440.6 KB	Display	wwPDB validaton report
Full document	8qjd_full_validation.pdf.gz	452.7 KB	Display
Data in XML	8qjd_validation.xml.gz	93.3 KB	Display
Data in CIF	8qjd_validation.cif.gz	127.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qj/8qjd ftp://data.pdbj.org/pub/pdb/validation_reports/qj/8qjd	HTTPS FTP

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Related structure data

Related structure data	8qjaC 8qjbC 8qjcC 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: Salmonella bongori Rhs core domain (residues 360-1420)

B: Salmonella bongori Rhs core domain (residues 360-1420)

hetero molecules

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

1

A: Salmonella bongori Rhs core domain (residues 360-1420)

hetero molecules

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

2

B: Salmonella bongori Rhs core domain (residues 360-1420)

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.071, 118.260, 131.757
Angle α, β, γ (deg.)	90.000, 105.520, 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 532 or resid 534...
d_2	ens_1	(chain "B" and (resid 360 through 532 or resid 534...

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	GLN	GLN	A	A	360 - 532	5 - 177
d_1	2	GLN	GLN	ASP	ASP	A	A	534 - 773	179 - 418
d_1	3	LEU	LEU	SER	SER	A	A	775 - 794	420 - 439
d_1	4	ASN	ASN	MET	MET	A	A	796 - 817	441 - 462
d_1	5	GLN	GLN	SER	SER	A	A	819 - 940	464 - 585
d_1	6	VAL	VAL	LEU	LEU	A	A	943 - 1050	588 - 695
d_1	7	GLN	GLN	HIS	HIS	A	A	1052 - 1174	697 - 819
d_1	8	VAL	VAL	VAL	VAL	A	A	1192	837
d_1	9	VAL	VAL	ILE	ILE	A	A	1194 - 1195	839 - 840
d_1	10	ASP	ASP	ILE	ILE	A	A	1197 - 1215	842 - 860
d_1	11	PRO	PRO	TYR	TYR	A	A	1222 - 1227	867 - 872
d_1	12	TRP	TRP	GLU	GLU	A	A	1229 - 1244	874 - 889
d_1	13	ARG	ARG	ILE	ILE	A	A	1246 - 1296	891 - 941
d_1	14	TRP	TRP	GLY	GLY	A	A	1298 - 1351	943 - 996
d_1	15	ASN	ASN	LEU	LEU	A	A	1353 - 1420	998 - 1065
d_2	1	GLU	GLU	GLN	GLN	B	B	360 - 532	5 - 177
d_2	2	GLN	GLN	ASP	ASP	B	B	534 - 773	179 - 418
d_2	3	LEU	LEU	SER	SER	B	B	775 - 794	420 - 439
d_2	4	ASN	ASN	MET	MET	B	B	796 - 817	441 - 462
d_2	5	GLN	GLN	SER	SER	B	B	819 - 940	464 - 585
d_2	6	VAL	VAL	LEU	LEU	B	B	943 - 1050	588 - 695
d_2	7	GLN	GLN	GLY	GLY	B	B	1052 - 1066	697 - 711
d_2	8	ASN	ASN	HIS	HIS	B	B	1078 - 1174	723 - 819
d_2	9	VAL	VAL	VAL	VAL	B	B	1192	837
d_2	10	VAL	VAL	ILE	ILE	B	B	1194 - 1195	839 - 840
d_2	11	ASP	ASP	ILE	ILE	B	B	1197 - 1215	842 - 860
d_2	12	PRO	PRO	TYR	TYR	B	B	1222 - 1227	867 - 872
d_2	13	TRP	TRP	GLU	GLU	B	B	1229 - 1244	874 - 889
d_2	14	ARG	ARG	ILE	ILE	B	B	1246 - 1296	891 - 941
d_2	15	TRP	TRP	GLY	GLY	B	B	1298 - 1351	943 - 996
d_2	16	ASN	ASN	LEU	LEU	B	B	1353 - 1420	998 - 1065

NCS oper: (Code: givenMatrix: (-0.990952459873, -0.047341981055, 0.125586460664), (-0.0515359208119, 0.998209648747, -0.030356976384), (-0.123924457386, -0.0365545343139, -0.991618119481)Vector: -12. ...

#1: Protein	Salmonella bongori Rhs core domain (residues 360-1420) Mass: 122700.406 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) / References: UniProt: S5MXP0
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1209 / Source method: isolated from a natural source / Formula: H₂O
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: 2.15 Å³/Da / Density % sol: 42.72 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein was diluted to 3 mg/ml using MonoQ buffer A and 1 ul was mixed with 2 ul of reservoir solution (0.1 M MES pH 7, 20% PEE 270, 3.67% acetone) in a hanging drop vapor diffusion ...Details: Protein was diluted to 3 mg/ml using MonoQ buffer A and 1 ul was mixed with 2 ul of reservoir solution (0.1 M MES pH 7, 20% PEE 270, 3.67% acetone) in a hanging drop vapor diffusion experiment at 19 deg C to obtain the crystals for the native dataset used for SIRAS phasing and for refinement. Before the diffraction experiment, crystals were cryoprotected by soaking in a solution consisting of 0.1M MES pH7 and 35% PEE270. For the Hg(II) derivative dataset used in SIRAS phasing, the crystal was grown in a similar fashion but using a reservoir solution comprising 0.1 M HEPES pH 7, 20% PEE 270. Derivatisation was performed by soaking the crystal for a couple of minutes in reservoir solution supplemented with 12.5 mM thimerosal. Crystals were back soaked and cryoprotected in mother liquor with an increased PEE 270 concentration (35%).

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.72 %

Crystal grow

Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein was diluted to 3 mg/ml using MonoQ buffer A and 1 ul was mixed with 2 ul of reservoir solution (0.1 M MES pH 7, 20% PEE 270, 3.67% acetone) in a hanging drop vapor diffusion ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.203→49.17 Å / Num. obs: 147230 / % possible obs: 99.61 % / Redundancy: 6.84 % / B_iso Wilson estimate: 37.86 Å² / CC_1/2: 0.999 / CC star: 1 / R_merge(I) obs: 0.08007 / R_pim(I) all: 0.03298 / R_rim(I) all: 0.08671 / Net I/σ(I): 17.62
Reflection shell	Resolution: 2.203→2.281 Å / R_merge(I) obs: 0.8547 / Mean I/σ(I) obs: 2.32 / Num. unique obs: 14230 / CC_1/2: 0.836 / CC star: 0.954 / R_rim(I) all: 0.9292 / % possible all: 97.11

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487+SVN	refinement
PHENIX	1.18.2_3874	refinement
Coot	0.9.3	model building
ARP/wARP		model building
BUCCANEER		phasing
SHARP		phasing
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

SIRAS / Resolution: 2.203→49.17 Å / SU ML: 0.2711 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.0092
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.211	14502	5.01 %
R_work	0.1822	274927	-
obs	0.1837	147188	99.31 %

Solvent computation

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

Displacement parameters

B_iso mean: 47.95 Å²

Refinement step

Cycle: LAST / Resolution: 2.203→49.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16859	0	2	1209	18070

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0036	17259
X-RAY DIFFRACTION	f_angle_d	0.6656	23430
X-RAY DIFFRACTION	f_chiral_restr	0.0461	2438
X-RAY DIFFRACTION	f_plane_restr	0.0055	3111
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8221	6360

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.412648743443 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 (%)
2.203-2.23	0.4004	422	0.3677	8146	X-RAY DIFFRACTION	88.43
2.23-2.25	0.3454	490	0.2935	9170	X-RAY DIFFRACTION	99.81
2.25-2.28	0.3075	480	0.2851	9164	X-RAY DIFFRACTION	99.79
2.28-2.31	0.3253	497	0.2747	9383	X-RAY DIFFRACTION	99.76
2.31-2.34	0.2888	479	0.2643	9065	X-RAY DIFFRACTION	99.77
2.34-2.37	0.3087	491	0.2547	9289	X-RAY DIFFRACTION	99.7
2.37-2.41	0.278	483	0.2388	9211	X-RAY DIFFRACTION	99.73
2.41-2.44	0.2899	481	0.2383	9136	X-RAY DIFFRACTION	99.78
2.44-2.48	0.2575	490	0.2272	9240	X-RAY DIFFRACTION	99.73
2.48-2.52	0.2378	481	0.2169	9167	X-RAY DIFFRACTION	99.78
2.52-2.56	0.2442	484	0.2178	9247	X-RAY DIFFRACTION	99.77
2.56-2.61	0.268	486	0.2098	9206	X-RAY DIFFRACTION	99.74
2.61-2.66	0.2376	483	0.2006	9146	X-RAY DIFFRACTION	99.78
2.66-2.72	0.2405	486	0.2018	9234	X-RAY DIFFRACTION	99.76
2.72-2.78	0.269	485	0.2068	9191	X-RAY DIFFRACTION	99.73
2.78-2.84	0.2585	492	0.2054	9240	X-RAY DIFFRACTION	99.6
2.84-2.91	0.2537	485	0.1991	9218	X-RAY DIFFRACTION	99.58
2.91-2.99	0.2216	483	0.1942	9159	X-RAY DIFFRACTION	99.57
2.99-3.08	0.2352	489	0.1904	9204	X-RAY DIFFRACTION	99.71
3.08-3.18	0.2242	485	0.1918	9180	X-RAY DIFFRACTION	99.71
3.18-3.29	0.23	486	0.1876	9229	X-RAY DIFFRACTION	99.59
3.29-3.42	0.2095	484	0.1857	9191	X-RAY DIFFRACTION	99.69
3.42-3.58	0.2109	488	0.1668	9154	X-RAY DIFFRACTION	99.67
3.58-3.77	0.1826	488	0.1526	9218	X-RAY DIFFRACTION	99.43
3.77-4	0.1725	479	0.1516	9193	X-RAY DIFFRACTION	99.65
4-4.31	0.1571	487	0.143	9221	X-RAY DIFFRACTION	99.61
4.31-4.74	0.1414	485	0.1277	9183	X-RAY DIFFRACTION	99.64
4.74-5.43	0.1598	486	0.1443	9189	X-RAY DIFFRACTION	99.73
5.43-6.84	0.2009	483	0.1703	9218	X-RAY DIFFRACTION	99.8
6.84-49.17	0.1815	484	0.1786	9135	X-RAY DIFFRACTION	99.13

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	0.459217637345	-0.215477152713	-0.274207079457	1.8274613333	0.0245309049711	0.724895889985	-0.0153268209872	0.0263385279753	0.0253492739126	-0.125038233404	0.0738971851811	-0.320783275009	-0.0488004640391	0.289045168824	-0.0590540915603	0.561811910975	-0.046445085681	-0.0256608810976	0.376969330545	-0.0199275553221	0.306861001644	2.55650851213	-36.9900971639	44.6240423574
2	0.201513823267	-0.00641522580667	0.178788039096	0.875007736055	0.34462420951	0.852962320173	0.0156423551273	0.0188791272359	0.0242231258144	-0.0888122307176	0.0652235756763	-0.120238295506	-0.0378540280746	0.168783026801	-0.0690148157144	0.497370924861	-0.0400460862897	-0.0135260447875	0.330107583309	-0.00186742021707	0.29169836957	-2.15741205254	-20.2706091352	64.9407521314
3	0.489517920544	-0.0241068828201	0.0876114710297	1.02221838883	0.287516370198	1.00225669295	-0.0116585538873	-0.109806628629	-0.0355739444007	0.352088108083	0.035844742578	0.0305097666557	0.0781225561336	-0.0685509086551	-0.0133028412163	0.630493678568	-0.0371210144238	-0.024451221814	0.304720999937	0.0244010525325	0.256042593664	-18.5573959654	-13.0988566163	97.9562317989
4	0.589376467856	0.648118335273	-0.226719103846	2.25850599593	-0.201733143846	0.506271173234	0.00817341963327	-0.00286274550201	0.087476041697	0.118766933383	0.0465710021398	0.371046641202	-0.115096497454	-0.182095182545	-0.0414741969491	0.54208325472	0.0421225428308	-0.0340560815493	0.368562239278	0.00227561281009	0.340741791245	-7.25634685451	23.7714886007	143.722284813
5	0.588079788542	-0.0790326818439	0.11969341525	1.14486133293	-0.150287507861	0.82502515279	0.0413393888893	-0.0825859752371	0.106760606921	0.37967007955	0.0518178821173	0.155937693528	-0.0635053392539	-0.194068050095	-0.0511707048744	0.556723583789	0.0509833212711	0.0976698994492	0.367143033078	0.0151484195733	0.370650766621	-9.51503161573	44.0002922892	137.727550329
6	1.92322736349	0.226804611118	0.332925691147	1.22738364298	-0.297876482863	0.431408604207	-0.00306733572686	-0.0727939007481	-0.0512695804179	-0.00489992054068	-0.00214492415151	-0.0407833302631	-0.0479199036869	-0.00616548998682	0.0356106875722	0.59986353274	0.0306681300036	-0.0484229630654	0.319223588393	-0.0161552760304	0.226012057509	8.3181906749	22.8922456077	121.103120191
7	0.433465880285	0.0938024957435	0.0111152629891	1.0332715723	-0.172943025649	0.903636785866	0.0223565397987	0.0453921012767	-0.0162389653889	-0.128665113171	0.0624347914616	0.199208833734	0.0566707832478	-0.174858061195	-0.0729284215214	0.423529793683	0.0239282624126	-0.0589215523582	0.275590247745	0.0259431537333	0.295465130365	0.971417992806	45.8308920446	105.017501892
8	0.717252531793	0.0958898818631	-0.0274053745536	1.96245317913	-0.151720768756	1.22206885221	-0.0294462076553	0.0593138083403	-0.0583901297946	-0.250071770095	0.00457021565194	-0.307241959468	0.00349768450829	0.223003185358	0.0220629067571	0.385345081791	0.0498677549612	0.0188768544296	0.296334659424	-0.0177011203593	0.248623898777	30.39558266	50.5422391798	98.7979750236
9	1.26242096579	-0.350452435606	0.0762436643116	1.54683263075	-0.109245220066	1.07833480895	0.00357211902307	0.230489818447	0.0223656602254	-0.420373587609	-0.0164519420766	-0.0187135428728	0.0135535313707	-0.0334057868416	0.0177317282363	0.561788622728	0.0299516162176	-0.0212844234188	0.297674694595	-0.00494197375102	0.252939282518	14.5991361372	49.8646601592	88.5154842952

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 517 )	A	A	360 - 517	1 - 158
2	2	chain 'A' and (resid 518 through 964 )	A	A	518 - 964	159 - 605
3	3	chain 'A' and (resid 965 through 1420 )	A	A	965 - 1420	606 - 1037
4	4	chain 'B' and (resid 360 through 517 )	B	B	360 - 517	1 - 158
5	5	chain 'B' and (resid 518 through 667 )	B	B	518 - 667	159 - 308
6	6	chain 'B' and (resid 668 through 819 )	B	B	668 - 819	309 - 460
7	7	chain 'B' and (resid 820 through 1023 )	B	B	820 - 1023	461 - 664
8	8	chain 'B' and (resid 1024 through 1204 )	B	B	1024 - 1204	665 - 820
9	9	chain 'B' and (resid 1205 through 1420 )	B	B	1205 - 1420	821 - 1036

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