PDB-9b8e: Structure of S-nitrosylated Legionella pneumophila Ceg10.

ID or keywords:

Entry

Database: PDB / ID: 9b8e

Title

Structure of S-nitrosylated Legionella pneumophila Ceg10.

Components

Ceg10

Keywords

HYDROLASE / Bacterial / effector / pathogen

Function / homology

ACETATE ION / Type IV secretion protein Dot

Function and homology information

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.4 Å

Authors

Tomchick, D.R. / Heisler, D.B. / Alto, N.M.

Funding support

United States, 6items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	1R35GM137978-01	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	1R21AI169558-01A1	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	R01AI083359	United States
Robert A. Welch Foundation	I-1704	United States
Burroughs Wellcome Fund	1011019	United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	T32 AI007520	United States

Citation

Journal: Plos Pathog. / Year: 2024
Title: Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery.
Authors: Embry, A. / Baggett, N.S. / Heisler, D.B. / White, A. / de Jong, M.F. / Kocsis, B.L. / Tomchick, D.R. / Alto, N.M. / Gammon, D.B.

History

Deposition	Mar 29, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 10, 2024	Provider: repository / Type: Initial release
Revision 1.1	May 29, 2024	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	9b8e_validation.pdf.gz	461 KB	Display	wwPDB validaton report
Full document	9b8e_full_validation.pdf.gz	463.6 KB	Display
Data in XML	9b8e_validation.xml.gz	21.6 KB	Display
Data in CIF	9b8e_validation.cif.gz	31.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b8/9b8e ftp://data.pdbj.org/pub/pdb/validation_reports/b8/9b8e	HTTPS FTP

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Related structure data

Related structure data	9b8dC 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: Ceg10

B: Ceg10

hetero molecules

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

1

A: Ceg10

hetero molecules

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

2

B: Ceg10

hetero molecules

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

Unit cell

Length a, b, c (Å)	103.416, 115.836, 40.878
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2
Space group name Hall	P22ab
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

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Protein , 1 types, 2 molecules AB

#1: Protein	Ceg10 Mass: 26837.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Cys159 is nitrosylated. / Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_00720 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA44XLE0

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Non-polymers , 5 types, 355 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.28 Å³/Da / Density % sol: 46.1 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 1,000, 0.1 M Tris, 25% ethylene glycol

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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: 0.97911 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.97911 Å / Relative weight: 1

Reflection

Resolution: 1.4→50 Å / Num. obs: 97458 / % possible obs: 99.8 % / Redundancy: 8.9 % / B_iso Wilson estimate: 13.24 Å² / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.058 / R_pim(I) all: 0.02 / R_rim(I) all: 0.061 / Χ²: 0.97 / Net I/σ(I): 8.1

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
1.4-1.42	8.4	0.887	4828	0.776	0.935	0.319	0.944	0.942	99.9
1.42-1.45	8.5	0.719	4817	0.832	0.953	0.258	0.765	0.944	99.9
1.45-1.48	8.6	0.599	4804	0.868	0.964	0.213	0.637	0.947	99.9
1.48-1.51	8.7	0.467	4821	0.916	0.978	0.165	0.496	0.988	99.7
1.51-1.54	8.2	0.4	4795	0.934	0.983	0.146	0.427	0.979	99.8
1.54-1.58	8.8	0.336	4836	0.958	0.989	0.118	0.357	0.979	99.9
1.58-1.62	9.3	0.301	4815	0.967	0.991	0.103	0.319	1	99.9
1.62-1.66	9.2	0.253	4836	0.978	0.994	0.086	0.267	1.001	100
1.66-1.71	9.1	0.21	4868	0.982	0.995	0.073	0.223	1.002	100
1.71-1.76	8.9	0.174	4804	0.987	0.997	0.061	0.185	1.016	99.8
1.76-1.83	8.3	0.136	4819	0.99	0.997	0.05	0.146	0.985	99.7
1.83-1.9	9.1	0.112	4846	0.994	0.998	0.039	0.119	1.016	99.8
1.9-1.99	9.4	0.091	4886	0.996	0.999	0.031	0.096	0.991	100
1.99-2.09	9.3	0.074	4857	0.997	0.999	0.025	0.078	0.971	99.9
2.09-2.22	9.1	0.06	4903	0.997	0.999	0.021	0.064	0.973	99.8
2.22-2.39	8.5	0.052	4871	0.997	0.999	0.019	0.055	0.968	99.5
2.39-2.63	9.5	0.045	4926	0.998	1	0.015	0.047	0.92	100
2.63-3.02	9.3	0.04	4943	0.999	1	0.014	0.043	0.912	100
3.02-3.8	8.7	0.035	4969	0.999	1	0.012	0.037	0.943	99.3
3.8-50	8.8	0.033	5214	0.999	1	0.011	0.035	0.925	99.2

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Processing

Software

Name	Version	Classification
PHENIX	1.21_5207	refinement
HKL-3000		data scaling
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.4→47.22 Å / SU ML: 0.1426 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1836	2000	2.11 %
R_work	0.1645	92912	-
obs	0.1649	94912	97.21 %

Solvent computation

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

Displacement parameters

B_iso mean: 20.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.4→47.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3639	0	34	345	4018

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0077	3830
X-RAY DIFFRACTION	f_angle_d	0.9066	5187
X-RAY DIFFRACTION	f_chiral_restr	0.0715	579
X-RAY DIFFRACTION	f_plane_restr	0.0097	673
X-RAY DIFFRACTION	f_dihedral_angle_d	12.8741	1423

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 (%)
1.4-1.43	0.287	104	0.2688	4839	X-RAY DIFFRACTION	71.75
1.43-1.47	0.24	135	0.2222	6271	X-RAY DIFFRACTION	93.15
1.47-1.52	0.2162	143	0.1898	6656	X-RAY DIFFRACTION	98.35
1.52-1.57	0.2285	145	0.1826	6733	X-RAY DIFFRACTION	99.54
1.57-1.62	0.1999	145	0.1659	6731	X-RAY DIFFRACTION	99.94
1.62-1.69	0.1874	146	0.169	6753	X-RAY DIFFRACTION	99.96
1.69-1.76	0.19	145	0.176	6755	X-RAY DIFFRACTION	99.81
1.76-1.86	0.2098	146	0.1642	6775	X-RAY DIFFRACTION	99.71
1.86-1.97	0.1653	147	0.1548	6806	X-RAY DIFFRACTION	99.94
1.97-2.13	0.1781	145	0.1491	6794	X-RAY DIFFRACTION	99.94
2.13-2.34	0.1738	147	0.1452	6805	X-RAY DIFFRACTION	99.53
2.34-2.68	0.1672	149	0.1482	6893	X-RAY DIFFRACTION	99.97
2.68-3.37	0.169	148	0.1641	6919	X-RAY DIFFRACTION	99.52
3.37-47.22	0.1813	155	0.168	7182	X-RAY DIFFRACTION	99.43

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	1.23482273781	-0.394864911072	-0.773054113565	1.36735459008	0.766420225875	2.78622114749	-0.0114989420601	0.176348290101	0.0302225822425	-0.0417885840298	-0.0138054372068	0.0501470097069	0.0140935666132	-0.168799282393	0.0262523664736	0.0474015272977	-0.0447778872993	-0.00132546069779	0.0737014094533	0.0135654876949	0.0699975330211	-19.7114644328	29.0197329337	-7.75790154505
2	8.03220519044	3.70539353281	-0.0517904951481	3.24283003794	0.789379412155	2.02833383962	0.106194362763	-0.237818537102	0.636769307864	0.0732182859119	-0.0272460285279	0.215062108489	-0.251372388921	-0.00166511253563	-0.0564175809025	0.15569422424	0.00163576622542	0.0184992630101	0.0745843289405	-0.016384569648	0.106725889709	-14.8491755139	43.5683707699	10.7361684381
3	2.91473029152	0.257026758648	-0.724731716597	1.30220258853	0.191404442168	1.63616036819	0.0564656754612	-0.0353165541129	-0.0145509720997	0.0907614253233	0.012261201523	-0.0671744154786	-0.0491792263118	0.105954452136	-0.0546790205778	0.067829185658	-0.0173516362302	-0.00854832526095	0.0717616695519	0.001348244402	0.0658849906557	-8.58381593513	35.1068672042	4.40901826546
4	3.40906327461	0.791442278389	0.347838287883	0.89903267804	0.358722525911	3.02922404522	0.0114596929574	0.119974153407	-0.00563167217147	-0.0378664012509	0.0750139555995	-0.116452518061	-0.0798352428477	0.132431484887	-0.0656985863285	0.0694174553555	-0.0184548205244	0.00576980686627	0.0692879528551	-0.00776273244001	0.06876067504	-8.94874553212	33.2019926025	-8.03018529216
5	8.74042586618	-0.787396626629	-4.26238870534	7.30457437999	-0.294169939274	8.66835104133	0.0418522139789	0.123657616798	0.359114533709	-0.150942452093	0.0274505306027	-0.406834933243	-0.327151262891	0.194608123166	-0.080900538108	0.129408081787	-0.0266420419806	-0.00563671501878	0.113915642232	0.00864261514129	0.0604184837605	-11.4315593806	35.6510867797	-20.452607022
6	5.7220865548	0.474033891501	3.44831260478	3.28865047104	0.0470076576779	4.24692803841	-0.12433487321	0.426550641674	0.609963180427	-0.160944425029	-0.0716460834312	0.179768477216	-0.486826475465	0.0117887346519	0.21307312406	0.150741671903	0.0195573776096	0.0363543033294	0.125608017173	0.0328291505767	0.111065308489	-12.622596749	42.8715722511	-10.8600490245
7	8.31976887629	0.873989221911	1.29733280548	4.17708279753	0.163814994445	7.53792538379	-0.170992826246	0.581720941228	0.385588229983	-0.201167589584	0.123055226613	0.0246744024788	-0.458243950798	0.334699011256	0.0110791674644	0.131301777365	-0.101052811577	0.00632960213825	0.209879925977	0.0203698202643	0.170554648508	4.2167323941	43.7298516563	-4.01956884092
8	3.31452764944	4.19079033276	0.79701796785	7.27471375376	1.33452046234	1.81908159311	0.302241255029	-0.452437108606	-0.594038077106	0.487500701853	0.0149326329402	0.219507376414	0.318979993817	-0.262553971481	-0.293596309273	0.191583233775	-0.0169019763335	-0.0703960351736	0.33355666087	0.0868875733421	0.419056055887	-0.917624025768	28.4074297072	7.46710521218
9	3.565310283	-0.133222503012	3.21038702731	0.676305391181	-0.130560131922	4.63952556752	-0.150983480174	-0.248989814842	0.205570180485	0.140800629676	0.0189681969907	0.065142995888	-0.288210517305	-0.405967935072	0.130162779854	0.124249069095	0.0199685593779	0.0183059574426	0.100520936214	0.0127766722185	0.0821191349366	-28.4826425888	21.9296276029	4.02329914124
10	5.46509715173	-0.987557509094	3.56868189402	3.22061387947	-1.82532031755	3.44538742998	-0.109613598927	-0.0100513512092	0.0373883751945	0.14555339388	-0.0666444742489	-0.284730246706	0.0402614697741	0.293878872829	0.126647014109	0.0777295652808	0.000147280947935	-0.00305335395336	0.0981777926234	-0.0133756898889	0.0909167150037	-13.5405870949	15.3644993965	-1.01479907707
11	4.06678430499	-3.9850585437	-4.03926959488	6.39438344353	3.56718974774	4.08839231854	0.0332831733227	-0.00727866460767	0.354640447705	-0.192308741294	0.109401791444	0.0524566813799	-0.198436190102	-0.104936143928	-0.139802484106	0.106589928129	0.00193229552838	-0.0234428010593	0.115994480511	0.000688685653147	0.0926140259934	-32.0841099461	21.8744260617	-10.4117998407
12	1.51481358867	-0.637845805526	0.423735469574	4.46992890099	-0.123681678787	1.74742181689	-0.023190561826	0.141965057611	-0.201020279819	-0.305290838123	0.0829093147834	0.353617700265	0.196398553597	-0.192690207489	-0.0469028368187	0.141289354061	-0.0426975907863	-0.0109123731255	0.118687600103	-0.00838364578142	0.085038625397	-30.0402328612	7.42459208977	-17.1015326444
13	0.663948817813	0.0768178741078	0.149469942373	2.79553085775	0.050657832986	3.17874656653	-0.00946557180739	-0.032035773054	-0.118238517746	-0.00413563888794	0.0952594852714	-0.175158599951	0.0927004315279	0.0603691478527	-0.0394422823515	0.0587016978658	-0.00706939182792	-0.00427833420992	0.0572325183577	-0.0159319560253	0.0880997614071	-21.054847619	8.44624826109	-2.50348151506
14	5.39395014411	-5.52074277685	1.18887431795	8.84827594895	-2.2161080647	8.03129554193	-0.0893908458155	-0.210086244193	-0.482131555471	0.166004082824	0.0951752812438	0.103629429621	0.444031129198	0.00694552503329	0.0047467336581	0.141126411888	-0.0192609402758	0.00681226612995	0.0849877472813	0.0114479045463	0.104311749259	-24.9683874947	9.42418636638	12.6569173143
15	3.23858342575	-1.26633890636	-1.55068804294	5.41452458291	3.63133976151	4.74764921002	-0.16715308521	-0.152843642353	-0.252475705124	0.18178224315	-0.0987998124021	0.527111001088	0.137368149657	-0.448606620701	0.262134578471	0.0909160151851	-0.0128473564688	-0.00028607571714	0.135535281873	0.0222323783648	0.104778474163	-31.6933965693	6.29021523589	2.81075895533
16	1.91648081934	-1.763465897	-0.738711368989	7.27193889076	-0.0843950310015	6.48506344632	-0.23840343621	-0.0708098500284	-0.22935579279	0.576317941893	0.189004899379	0.320360143095	0.310974097667	-0.356960284022	0.0273618572524	0.278377948826	-0.0194844049079	-0.0145481838577	0.10818809271	0.00642473081446	0.243708222375	-25.884660344	-7.07419840974	-1.44776405977
17	3.44130371023	3.73275970793	-2.17314925741	8.94703384506	-4.91177367308	4.821635298	-0.076074551354	0.326827817195	-0.230208111786	-0.77407257428	0.302506173513	-0.751099194126	-0.125554082675	0.261419674026	-0.210293425118	0.344136371589	-0.041694181668	0.0939997993514	0.180321615884	-0.112486929805	0.374356223789	-18.1089827855	-5.82186090741	-13.8976685914
18	2.73146930248	1.66252863371	-0.206822415545	7.66538926146	4.69044886225	4.20715349011	-0.0534645874239	0.695989990452	-0.240696243583	0.0904449214884	0.589941360423	-1.25286540201	0.140918317922	0.357091477534	-0.481752812517	0.446710956074	0.0362020016643	0.187112277485	0.356959503014	-0.0293527358784	0.433439538547	-11.0735720132	9.44860235091	-14.8774911178

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 57 through 115 )	A	A	57 - 115	1 - 59
2	2	chain 'A' and (resid 116 through 139 )	A	A	116 - 139	60 - 83
3	3	chain 'A' and (resid 140 through 175 )	A	A	140 - 175	84 - 119
4	4	chain 'A' and (resid 176 through 212 )	A	A	176 - 212	120 - 156
5	5	chain 'A' and (resid 213 through 225 )	A	A	213 - 225	157 - 169
6	6	chain 'A' and (resid 226 through 238 )	A	A	226 - 238	170 - 182
7	7	chain 'A' and (resid 239 through 264 )	A	A	239 - 264	183 - 202
8	8	chain 'A' and (resid 265 through 284 )	A	A	265 - 284	203 - 222
9	9	chain 'B' and (resid 57 through 86 )	B	G	57 - 86	1 - 30
10	10	chain 'B' and (resid 87 through 105 )	B	G	87 - 105	31 - 49
11	11	chain 'B' and (resid 106 through 115 )	B	G	106 - 115	50 - 59
12	12	chain 'B' and (resid 116 through 158 )	B	G	116 - 158	60 - 102
13	13	chain 'B' and (resid 159 through 212 )	B	G	159 - 212	103 - 156
14	14	chain 'B' and (resid 213 through 225 )	B	G	213 - 225	157 - 169
15	15	chain 'B' and (resid 226 through 238 )	B	G	226 - 238	170 - 182
16	16	chain 'B' and (resid 239 through 258 )	B	G	239 - 258	183 - 199
17	17	chain 'B' and (resid 259 through 272 )	B	G	259 - 272	200 - 213
18	18	chain 'B' and (resid 273 through 284 )	B	G	273 - 284	214 - 225

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