PDB-8gmh: Crystal Structure of the ternary complex of TelA-LXG, LapA3, and LapA4

ID or keywords:

Entry

Database: PDB / ID: 8gmh

Title

Crystal Structure of the ternary complex of TelA-LXG, LapA3, and LapA4

Components

LXG domain-containing protein
LapA3
LapA4

Keywords

PROTEIN BINDING / Type VII secretion / protein secretion / bacterial toxin / targeting factors / signal sequence

Function / homology

LXG domain / LXG domain of WXG superfamily / LXG domain profile. / Variable surface protein mvspG / LXG domain-containing protein

Function and homology information

Biological species

Streptococcus intermedius B196 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Klein, T.A. / Shah, P.Y. / Gkragkopoulou, P. / Grebenc, D.W. / Kim, Y. / Whitney, J.C.

Funding support

Canada, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Structure of a tripartite protein complex that targets toxins to the type VII secretion system.
Authors: Klein, T.A. / Shah, P.Y. / Gkragkopoulou, P. / Grebenc, D.W. / Kim, Y. / Whitney, J.C.

History

Deposition	Mar 25, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8gmh.cif.gz	419.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8gmh.ent.gz	286.9 KB	Display	PDB format
PDBx/mmJSON format	8gmh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8gmh_validation.pdf.gz	479.4 KB	Display	wwPDB validaton report
Full document	8gmh_full_validation.pdf.gz	482.7 KB	Display
Data in XML	8gmh_validation.xml.gz	32.1 KB	Display
Data in CIF	8gmh_validation.cif.gz	45.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gm/8gmh ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gmh	HTTPS FTP

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Related structure data

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

B: LXG domain-containing protein

C: LapA4

D: LapA3

A: LXG domain-containing protein

E: LapA4

F: LapA3

hetero molecules

102 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: LXG domain-containing protein

C: LapA4

D: LapA3

hetero molecules

defined by author&software
Evidence: gel filtration
51.1 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: LXG domain-containing protein

E: LapA4

F: LapA3

defined by author&software
50.9 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	51.925, 61.419, 97.916
Angle α, β, γ (deg.)	77.680, 77.140, 65.060
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1

#1: Protein	LXG domain-containing protein Mass: 25821.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius B196 (bacteria) Gene: SIR_0169 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZCZ9
#2: Protein	LapA4 Mass: 15547.171 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius B196 (bacteria) Gene: SIR_0166.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Protein	LapA3 Mass: 9527.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius B196 (bacteria) Gene: SIR_0167 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1ZBE7
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.71 Å³/Da / Density % sol: 54.65 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.02M Magnesium chloride 0.1M HEPES:NaOH pH 7.5 22% (w/v) polyacrylic acid 5100

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 1, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 31528 / % possible obs: 97.2 % / Redundancy: 3.7 % / B_iso Wilson estimate: 41.45 Å² / CC_1/2: 0.948 / CC star: 0.986 / R_merge(I) obs: 0.209 / R_pim(I) all: 0.123 / R_rim(I) all: 0.243 / Χ²: 1.725 / Net I/σ(I): 3.9 / Num. measured all: 117339

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
2.6-2.64	2.7	0.858	1504	0.478	0.804	0.586	1.045	0.608	92.9
2.64-2.69	2.9	0.849	1534	0.487	0.809	0.564	1.025	0.572	94.7
2.69-2.74	3.1	0.792	1562	0.624	0.877	0.506	0.944	0.614	94.8
2.74-2.8	3.1	0.655	1558	0.667	0.895	0.413	0.779	0.69	96.3
2.8-2.86	3.5	0.622	1564	0.743	0.923	0.38	0.732	0.707	96.5
2.86-2.93	3.9	0.554	1614	0.805	0.944	0.321	0.642	0.7	97.6
2.93-3	3.9	0.518	1543	0.828	0.952	0.299	0.599	0.751	97.9
3-3.08	4	0.445	1615	0.848	0.958	0.253	0.513	0.753	97.9
3.08-3.17	4	0.386	1559	0.889	0.97	0.22	0.445	0.832	97.7
3.17-3.28	3.9	0.349	1585	0.897	0.972	0.201	0.404	0.826	97.7
3.28-3.39	3.9	0.311	1593	0.903	0.974	0.18	0.36	1.031	97.6
3.39-3.53	3.7	0.239	1567	0.933	0.983	0.141	0.278	1.263	96.7
3.53-3.69	4.1	0.204	1613	0.953	0.988	0.115	0.234	1.498	98.7
3.69-3.88	4	0.187	1565	0.954	0.988	0.105	0.215	1.864	98.4
3.88-4.13	4	0.167	1602	0.954	0.988	0.096	0.193	2.032	98.3
4.13-4.45	3.9	0.156	1587	0.956	0.989	0.092	0.182	2.66	97.8
4.45-4.89	3.9	0.153	1565	0.958	0.989	0.089	0.178	2.894	97
4.89-5.6	4.1	0.156	1627	0.968	0.992	0.09	0.181	2.843	99
5.6-7.05	3.9	0.156	1570	0.966	0.991	0.092	0.182	3.156	98
7.05-50	4	0.122	1601	0.978	0.994	0.072	0.142	6.272	98.1

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
HKL-3000		data scaling
HKL-3000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→45.08 Å / SU ML: 0.3873 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.1625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2577	1479	4.71 %
R_work	0.2147	29935	-
obs	0.2168	31414	96.25 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.6→45.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6614	0	12	275	6901

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0014	6693
X-RAY DIFFRACTION	f_angle_d	0.2998	9105
X-RAY DIFFRACTION	f_chiral_restr	0.0306	1132
X-RAY DIFFRACTION	f_plane_restr	0.002	1173
X-RAY DIFFRACTION	f_dihedral_angle_d	12.6017	2364

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 (%)
2.6-2.68	0.3767	91	0.3091	2456	X-RAY DIFFRACTION	86.08
2.68-2.78	0.3383	127	0.2796	2675	X-RAY DIFFRACTION	94.38
2.78-2.89	0.2971	113	0.2507	2738	X-RAY DIFFRACTION	96.16
2.89-3.02	0.3139	138	0.2494	2768	X-RAY DIFFRACTION	97.94
3.02-3.18	0.3055	141	0.2531	2758	X-RAY DIFFRACTION	97.74
3.18-3.38	0.3037	153	0.2594	2735	X-RAY DIFFRACTION	97.47
3.38-3.64	0.2988	144	0.2201	2756	X-RAY DIFFRACTION	97.41
3.64-4.01	0.2469	123	0.1957	2816	X-RAY DIFFRACTION	98.49
4.01-4.58	0.2365	146	0.1725	2707	X-RAY DIFFRACTION	97.34
4.59-5.77	0.2001	155	0.1847	2796	X-RAY DIFFRACTION	98.53
5.77-45.08	0.2099	148	0.187	2730	X-RAY DIFFRACTION	97.16

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	6.34675615024	3.56224314746	1.95522653264	2.96434476263	1.59981476803	1.50363242619	0.0619430617226	-0.370773651484	0.0351659138874	0.0796656854815	-0.129079621387	0.327870596163	0.224843969336	-0.225997547336	0.0570504577985	0.449521409787	-0.0971277857272	-0.0117376104734	0.306121695433	0.010732044563	0.357027506379	22.7399073935	26.3286329415	34.3301637355
2	2.79165595122	3.13986423835	2.39549501463	2.59526694498	1.11265388211	1.51609975804	-0.201220546712	-0.0326385986215	0.422966536091	-0.233506577693	-0.0815914434543	0.150194157713	-0.647666724943	0.332018717377	0.210243111412	0.531241019765	-0.243557434386	-0.0229031633476	0.527732090865	-0.0335096540829	0.539551519251	-17.6424364919	1.11955665057	15.41369886
3	7.17456973769	3.63562567444	2.36382381957	5.52065159409	0.523478825356	2.90741000407	-0.491050468033	0.160557417668	1.06858385072	-0.394743675151	0.363744276135	0.978536916767	-0.0795350246009	-0.0963685557895	0.0796852015054	0.431879981323	-0.0463285995884	-0.0301393242333	0.31121393484	-0.0550565555346	0.505618146602	24.9169639942	39.4953218981	29.125581172
4	7.58156061667	4.66325612683	1.83384046732	4.4349040864	1.17918446057	1.90336751285	-0.197149516665	-0.154575870617	0.0595061331648	-0.0388980067486	0.0697070542864	-0.121983310909	-0.150413119105	0.0319842866453	0.0595311493508	0.283644073875	0.0248325498937	-0.0123825275027	0.19927930884	-0.0684538408651	0.275286613806	-46.8623284749	-25.1951818149	6.7804014592
5	6.56345466788	5.06342870843	2.56494541033	4.85139185573	2.11000566557	1.95278527154	0.428892409626	-0.517486810675	-0.532991689825	0.362898897238	-0.305115546614	-0.495823266705	-0.077693362539	-0.0278977092563	-0.0639573759352	0.3496846715	-0.0206854287878	0.000644000752053	0.268291523542	0.0160375981856	0.341852032954	-36.1434266477	-20.3037176857	15.0807436559
6	5.85711832318	1.48992053903	2.24046615801	4.28398426333	3.31835470446	3.05879301019	-0.189652279036	-0.107650784004	-0.519679947352	0.747839051523	0.113766144127	0.0177164501759	0.33222572337	0.92794261068	0.0300665926351	0.436446442119	-0.0850611814904	-0.0105136455423	0.519895695622	-0.00331267267548	0.585313049849	45.7914505889	31.862046446	37.9287285339
7	8.55905359139	4.8033826066	1.77746096303	3.47975741003	0.7660541477	1.88990153845	-0.604334231618	1.26094572186	-1.22187106804	-0.467627069776	0.752121409252	-0.74487081795	0.21865908537	0.146677298767	-0.246469557666	0.560850829808	-0.206705100198	0.0587739486984	0.466772981717	-0.136932902877	0.889217813706	18.2511844532	13.5028202736	24.5859406302
8	6.68144794325	5.48419990061	0.351706971117	4.53036211438	0.456355085229	2.18219796749	-0.588716620724	1.11004507832	0.422348133185	-0.317433291044	0.583793816531	0.288403242034	-0.217308741187	0.436418187133	-0.00187663513285	0.488750608006	-0.0976007093153	0.0732172665328	0.451120163309	-0.0976485911493	0.484580510851	35.5942976353	31.833311096	27.733531573
9	6.04866014439	-3.87651335955	-2.87149337463	3.90857724064	2.02696202713	2.15231559209	0.0248311689924	0.504653298658	0.266945966349	-0.136772907393	-0.0133369867335	0.285883160199	-0.189362551658	-0.289530276799	-0.0204122202306	0.411056440332	0.0879192362399	-0.00214121359508	0.323357346282	-0.0158395739637	0.511715479671	22.6210413482	-26.5845730605	-34.7187145007
10	2.76165674011	-2.58111201304	-2.22144923565	2.69456606089	1.4576359461	1.45361815553	-0.272401252814	-0.244185858403	-0.400113119895	0.225689864093	0.03725098765	0.0624592913143	0.431411667011	0.463358488165	0.20712367351	0.474150636015	0.242948157567	0.0291978066869	0.543059716778	0.00646248228085	0.506343117243	-17.7397462072	-1.30081341747	-15.7716218408
11	7.41598135018	-3.65887073155	-2.16866591945	5.96524603978	1.89250187901	3.13048990583	-0.253795146773	-0.163477192163	-1.28800973743	0.172374241935	0.184680526905	1.25720775406	-0.066831425393	-0.157252574141	0.0104850258055	0.490099894535	0.0801951331312	0.00670324798159	0.313795597975	-0.0432323473804	0.580598021107	24.630968873	-39.6025386264	-29.4417335138
12	4.46755368319	-4.05256709274	-0.810862434386	3.79814085909	0.279011899699	1.13108672843	0.0326701263512	0.0484112911689	-0.16010754892	-0.160979315197	0.0293851973676	0.0173817208276	-0.0350113103042	-0.110313577321	-0.0578691534195	0.289647800792	-0.0283303105021	-0.0143353659379	0.340984439668	-0.153049250746	0.428538661134	-52.2470576518	27.7648967	-5.77466431784
13	1.38679660507	0.0761631910331	-0.728354892887	-0.0235709703307	-0.0560124551766	0.351924455621	0.424055531581	0.211879900446	0.481199104984	0.206265012306	0.0543573471903	-1.01992034677	0.647632591762	0.230904865837	-0.333306985776	0.685082825769	0.378085712921	0.0611362328082	0.700625860941	-0.153127694284	1.02169998422	-7.92714825857	4.62620031578	-19.7845407891
14	5.98602260557	-5.47157602871	-2.8686723134	4.85127017119	2.79669498808	1.66332323614	0.702464964787	0.574757394436	0.250604595105	-0.70500010238	-0.540788876319	-0.196695265175	-0.253065715756	-0.156375620182	-0.152256920691	0.393530580708	0.0766869777023	0.0661362960413	0.348698112426	0.0257493307427	0.468550030572	-40.6342654093	22.4227521773	-14.5521474133
15	6.15803609095	-3.03054687321	-2.56163629668	7.8468774327	1.23929898287	8.89870067078	-0.0797856153649	-0.0233127813781	0.144654239344	-0.26771613323	0.0799963260757	-0.03321676446	-0.378492031603	1.17682554551	0.178444038871	0.377943108462	-0.00254344357756	-0.0845205746646	0.524063285053	-0.0729184972623	0.588115609838	45.8311390534	-32.1722885522	-38.3516766677
16	3.36070279138	-3.04607461685	-3.0233107284	2.74511167166	2.76498720623	3.82093542098	-0.427471058149	-0.773971308845	1.09079840971	0.165070811487	0.898073752709	-0.255891193759	-0.188021951345	0.196924087358	-0.409893157707	0.499245217496	0.156090603099	-0.0218782862991	0.432845432911	-0.0433701877534	0.964077723435	18.1473147495	-13.768747352	-24.9958908158
17	4.92229698851	-2.77550838918	-0.655951139936	4.15646491932	0.291031606326	3.31096070151	-0.378597169683	-1.08307902211	-0.131653211577	0.0626560889371	0.52534658473	0.074429777065	0.0966232776819	0.515924080509	-0.0901547978502	0.447052700633	0.157003018443	-0.0846147504701	0.469418860061	-0.1417714967	0.527950879027	35.5198370775	-31.9415480195	-28.1789334482

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 'B' and (resid 1 through 86 )	B	A	1 - 86	1 - 86
2	2	chain 'B' and (resid 87 through 166 )	B	A	87 - 166	87 - 166
3	3	chain 'B' and (resid 167 through 222 )	B	A	167 - 222	167 - 222
4	4	chain 'C' and (resid 2 through 62 )	C	E	2 - 62	1 - 61
5	5	chain 'C' and (resid 63 through 139 )	C	E	63 - 139	62 - 138
6	6	chain 'D' and (resid 5 through 23 )	D	F	5 - 23	1 - 19
7	7	chain 'D' and (resid 24 through 38 )	D	F	24 - 38	20 - 34
8	8	chain 'D' and (resid 39 through 82 )	D	F	39 - 82	35 - 78
9	9	chain 'A' and (resid 1 through 86 )	A	G	1 - 86	1 - 86
10	10	chain 'A' and (resid 87 through 166 )	A	G	87 - 166	87 - 166
11	11	chain 'A' and (resid 167 through 223 )	A	G	167 - 223	167 - 223
12	12	chain 'E' and (resid 2 through 54 )	E	H	2 - 54	1 - 53
13	13	chain 'E' and (resid 55 through 72 )	E	H	55 - 72	54 - 71
14	14	chain 'E' and (resid 73 through 138 )	E	H	73 - 138	72 - 137
15	15	chain 'F' and (resid 5 through 23 )	F	I	5 - 23	1 - 19
16	16	chain 'F' and (resid 24 through 38 )	F	I	24 - 38	20 - 34
17	17	chain 'F' and (resid 39 through 82 )	F	I	39 - 82	35 - 78

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Feb 9, 2022. New format data for meta-information of EMDB entries

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