PDB-4qn8: The crystal structure of an effector protein VipE from Legionella...

ID or keywords:

Entry

Database: PDB / ID: 4qn8

Title

The crystal structure of an effector protein VipE from Legionella pneumophila subsp. pneumophila str. Philadelphia 1

Components

VipE

Keywords

SIGNALING PROTEIN / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG

Function / homology

: / Effector protein VipE / BETA-MERCAPTOETHANOL / VipE

Function and homology information

Biological species

Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.751 Å

Authors

Tan, K. / Xu, X. / Cui, H. / Liu, S. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of an effector protein VipE from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Authors: Tan, K. / Xu, X. / Cui, H. / Liu, S. / Savchenko, A. / Joachimiak, A.

History

Deposition	Jun 17, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Mar 26, 2025	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4qn8.cif.gz	200.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4qn8.ent.gz	163.8 KB	Display	PDB format
PDBx/mmJSON format	4qn8.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/qn/4qn8 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/4qn8	HTTPS FTP

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Related structure data

Similar structure data	7doc-2 6byf-5 5zob-2 6byf-4 5hpf-3 5zms-1 6fud-d 2kbf-d 5hpf-2 2i6o-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC105584

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#234 - Jun 2019 MDM2 and Cancer similarity (1) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #9 - Sep 2000 Lysozyme similarity (1)

Deposited unit

A: VipE

B: VipE

C: VipE

hetero molecules

53 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: VipE

hetero molecules

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

2

B: VipE

hetero molecules

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

3

C: VipE

hetero molecules

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

Unit cell

Length a, b, c (Å)	77.553, 77.553, 71.997
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

Details

THE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. The protein is predicted to be monomeric.

#1: Protein	VipE Mass: 17548.945 Da / Num. of mol.: 3 / Fragment: UNP residues 1-153 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / Gene: lpg2813, vipE / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q5ZRR7
#2: Chemical	ChemComp-BME / BETA-MERCAPTOETHANOL Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.37 Å³/Da / Density % sol: 48.2 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris, 1.5M Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 16, 2012 / Details: mirror
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 1.75→30.5 Å / Num. all: 48733 / Num. obs: 48733 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / B_iso Wilson estimate: 23.5 Å² / R_merge(I) obs: 0.085 / Net I/σ(I): 24.4
Reflection shell	Resolution: 1.75→1.78 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.629 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
SHELXD		phasing
MLPHARE		phasing
DM		model building
ARP		model building
WARP		model building
HKL-3000		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
DM		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.751→30.434 Å / SU ML: 0.23 / σ(F): 1.96 / Phase error: 25.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2334	2446	5.04 %
R_work	0.1897	-	-
obs	0.1919	48568	99.53 %
all	-	48569	-

Solvent computation

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

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.98 Å²	0 Å²	-0 Å²
2-	-	2.98 Å²	0 Å²
3-	-	-	-5.9601 Å²

Refinement step

Cycle: LAST / Resolution: 1.751→30.434 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3542	0	16	364	3922

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3674
X-RAY DIFFRACTION	f_angle_d	1.055	4984
X-RAY DIFFRACTION	f_dihedral_angle_d	13.381	1384
X-RAY DIFFRACTION	f_chiral_restr	0.069	574
X-RAY DIFFRACTION	f_plane_restr	0.006	655

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 (%)
1.751-1.7864	0.3447	152	0.2688	2691	X-RAY DIFFRACTION	99
1.7864-1.8252	0.3422	130	0.2493	2734	X-RAY DIFFRACTION	100
1.8252-1.8677	0.3048	146	0.2458	2704	X-RAY DIFFRACTION	100
1.8677-1.9144	0.3175	130	0.2653	2718	X-RAY DIFFRACTION	99
1.9144-1.9661	0.3086	159	0.2452	2705	X-RAY DIFFRACTION	99
1.9661-2.024	0.2838	122	0.2066	2704	X-RAY DIFFRACTION	100
2.024-2.0893	0.2672	164	0.1975	2741	X-RAY DIFFRACTION	100
2.0893-2.1639	0.2726	135	0.1908	2743	X-RAY DIFFRACTION	100
2.1639-2.2505	0.2527	130	0.2066	2703	X-RAY DIFFRACTION	99
2.2505-2.3529	0.2469	139	0.1944	2712	X-RAY DIFFRACTION	99
2.3529-2.4769	0.2385	145	0.1951	2702	X-RAY DIFFRACTION	100
2.4769-2.632	0.2486	149	0.1774	2734	X-RAY DIFFRACTION	100
2.632-2.8351	0.2262	131	0.1895	2713	X-RAY DIFFRACTION	100
2.8351-3.1202	0.2325	176	0.1879	2729	X-RAY DIFFRACTION	100
3.1202-3.5711	0.2081	133	0.1812	2719	X-RAY DIFFRACTION	100
3.5711-4.4968	0.1915	165	0.1587	2705	X-RAY DIFFRACTION	100
4.4968-30.4383	0.1967	140	0.1737	2665	X-RAY DIFFRACTION	98

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	3.4219	3.0267	-0.2447	6.2978	-1.0363	1.8115	-0.1547	0.1823	-0.1999	-0.2737	-0.0457	0.1664	-0.1201	-0.3401	0.1242	0.1647	0.0493	-0.0282	0.2924	-0.0533	0.1756	-17.0486	49.4541	3.8035
2	1.3061	1.3681	-0.9899	4.1307	0.6173	1.7587	0.0618	0.167	0.1094	-0.2774	-0.2518	0.3125	-0.3531	-0.1874	0.1724	0.2416	0.0065	-0.044	0.2214	-0.0106	0.2252	-11.5136	62.8006	6.4598
3	2.2149	2.0144	0.6444	7.9586	-0.5831	1.7518	0.3976	-0.1022	0.1214	0.7623	-0.2528	1.0007	-0.4924	-0.6635	-0.1027	0.2898	0.0683	0.115	0.3227	0.0279	0.2301	-18.2403	51.5016	17.5412
4	3.7567	0.5223	2.5976	4.1555	-3.2103	9.4897	0.4979	0.0657	-0.198	0.0621	0.5111	1.1086	0.6379	-0.119	-0.6341	0.2604	-0.1047	-0.035	0.3472	-0.0024	0.3492	-18.3121	34.7173	19.8429
5	1.7511	1.0436	-0.5085	1.9038	-1.1724	2.8321	0.0381	-0.206	-0.2284	0.0222	-0.0767	0.1319	0.0357	-0.2403	0.0257	0.0931	0.0018	0.0192	0.2058	0.0092	0.1475	-12.7185	44.4405	10.9904
6	1.0721	-1.2104	-0.4838	6.5548	5.1748	7.2063	-0.0208	-0.0004	0.0992	-0.6388	0.1813	-0.138	-0.5362	0.4265	-0.2135	0.1857	-0.0288	0.0161	0.1554	0.0219	0.1453	-1.47	57.7847	6.6086
7	3.2924	-0.4102	-1.3761	2.9341	1.0039	2.5951	-0.0119	-0.6476	0.1757	1.1206	0.3712	0.3022	-0.0418	-0.1907	-0.0887	0.3972	0.0823	0.0743	0.2709	-0.0135	0.1685	-5.575	56.5681	24.3432
8	3.7796	-0.9634	-2.0366	3.3925	2.0324	2.9727	0.0669	-0.056	-0.0778	0.0383	-0.049	-0.1624	-0.0604	0.2637	-0.0237	0.1729	-0.0032	0.0054	0.1445	0.019	0.0994	-0.8815	49.3533	11.5383
9	1.5458	-0.7869	0.4392	5.7114	4.1691	4.8515	0.0299	0.1819	0.0821	-0.2623	0.1483	-0.6842	-0.2812	0.9822	-0.1833	0.1302	-0.0787	0.0274	0.2949	0.0276	0.2282	7.5386	53.2729	10.6941
10	6.2034	-6.2022	5.7068	6.2316	-5.6767	5.2701	-0.2891	-0.2319	0.5666	0.2682	0.058	-0.6865	-0.7384	0.0755	0.2995	0.2344	0.0048	-0.0361	0.1953	-0.0544	0.1879	4.0129	60.5305	22.1109
11	3.4791	2.1084	1.6148	4.5068	3.0977	6.8856	-0.074	-0.184	-0.0869	0.2204	0.0587	-0.2912	0.3247	0.2088	-0.1268	0.1391	0.046	0.0078	0.1025	0.0261	0.1334	2.759	45.6555	19.4812
12	8.3372	0.0765	1.8725	2.0872	-0.2133	2.4828	0.0824	-0.3884	0.0663	0.4615	-0.0053	0.0613	0.0141	-0.2654	-0.0772	0.3831	-0.0113	0.0503	0.2067	-0.0047	0.1762	-5.2676	72.2377	17.9016
13	6.8197	2.5787	0.8703	3.0597	1.7313	4.4014	-0.1019	0.4602	-0.3712	0.0561	-0.0095	-0.8445	0.7477	0.3052	0.13	0.3878	0.0749	-0.0153	0.1839	0.0368	0.3137	9.0945	70.1804	15.163
14	3.6422	-4.2964	3.5569	5.0511	-4.0524	4.6235	-0.1262	0.6246	-0.5271	-0.3417	0.1379	0.1591	0.0392	-0.2504	-0.0416	0.3446	-0.0393	0.007	0.2742	-0.0476	0.1743	-4.7164	70.5896	4.3609
15	3.8012	-5.3201	-3.6607	9.9693	1.806	7.8564	0.1429	0.4979	-0.0145	-0.6158	-0.1167	1.3471	-0.2228	-1.1851	-0.0697	0.2532	-0.0122	-0.0261	0.3151	0.0566	0.4484	-18.4741	80.036	1.8489
16	5.4131	1.7463	4.6509	3.0876	0.829	7.7855	-0.0105	-0.0503	0.3586	0.0657	0.0032	0.3731	0.0657	-0.4158	0.0298	0.1631	-0.0227	0.0176	0.1281	0.0139	0.2077	-7.205	78.7235	10.7255
17	5.0882	-0.3648	-2.8063	6.2862	2.351	5.5636	-0.1316	-0.2577	0.0958	0.2154	0.0795	-0.5161	0.0841	0.5772	-0.0413	0.1698	0.047	-0.0477	0.2203	0.0286	0.2286	10.0294	81.2694	15.015
18	4.9116	-0.4353	-0.2718	4.8385	0.767	6.5272	-0.0221	0.4395	-0.1784	-0.3343	0.1234	-0.3925	0.5135	0.2154	-0.1286	0.2115	-0.0078	0.0216	0.1941	0.0165	0.1679	4.9083	82.4268	4.3731
19	8.5075	-4.3115	-5.8289	6.1373	4.7252	6.9838	0.2614	-0.1162	0.96	-0.2611	0.1689	-0.9985	-0.8856	1.0782	-0.3019	0.2189	-0.0683	-0.0272	0.2559	0.0141	0.323	10.9791	91.4089	11.1254
20	7.3524	-1.0969	-0.2269	4.1824	-0.1698	6.4613	-0.1419	0.5831	0.2825	-0.4611	0.0127	-0.5932	-0.3498	0.625	0.1619	0.182	-0.0582	0.0291	0.1865	0.0052	0.2603	12.186	88.7952	-1.4839
21	5.1867	1.577	-3.0815	1.7322	-1.3689	3.3843	-0.0199	0.1992	0.0835	-0.0106	-0.1107	0.1877	-0.5407	-0.8686	-0.1377	0.2329	0.0454	-0.0363	0.1878	-0.0002	0.2292	-3.0157	90.2242	6.2402
22	2.5247	0.5532	1.2724	2.4085	0.6109	3.091	-0.8337	0.2906	-0.6981	-0.4876	0.1954	0.5374	0.0925	-0.4617	-0.1831	0.4161	-0.1194	0.3014	0.2972	0.1116	0.6069	-41.3032	49.5336	19.266
23	3.6567	-0.8296	0.4655	3.1757	1.1561	4.8923	-0.4714	-0.9465	-1.1433	0.6916	0.1432	0.0797	0.8471	-0.0247	0.1011	0.2202	0.0305	0.1585	0.2737	0.1313	0.4379	-28.2403	48.9694	15.8331
24	8.6887	-1.7427	4.652	1.3609	-1.672	3.0344	0.5711	0.4616	-1.5628	-1.0918	-0.297	0.5079	0.641	-0.2993	-1.0048	0.5868	-0.2739	-0.1126	0.6095	-0.1306	0.6309	-42.7309	47.4388	5.3368
25	0.6071	0.0067	-0.1059	0.0068	0.0539	0.4432	-0.0236	-0.4176	-0.0632	-0.1862	0.1927	0.4574	0.1202	-0.5174	-0.3552	0.2358	-0.3329	-0.1322	1.2208	0.1264	0.7411	-55.6831	55.7837	6.8948
26	1.8183	-0.0123	1.6189	2.9645	0.3601	2.0364	-0.0332	0.5749	-0.5479	-0.0189	0.0118	0.6224	0.4648	-1.1148	-0.1052	0.1446	-0.2058	-0.0042	0.58	-0.0925	0.3737	-44.4228	54.8755	11.7919
27	5.4822	-3.0478	-5.1581	3.7428	1.7411	6.7973	-0.0071	-0.4329	-0.1055	0.0928	-0.0753	-0.2134	-0.0151	0.4248	0.0138	0.1407	-0.0571	-0.0226	0.2227	0.042	0.1925	-27.6452	59.7142	15.1945
28	2.9318	-1.1644	-0.8938	2.9089	0.0375	1.6506	0.3305	0.497	-0.2907	-0.4394	-0.4502	0.1695	-0.1502	-0.3007	0.0704	0.2	0.015	-0.0265	0.2877	-0.0343	0.1642	-33.3092	59.8648	4.756
29	6.5515	-4.1366	-4.8849	4.2915	4.7584	6.0206	0.6719	-0.2796	0.5734	-0.3204	0.0671	-0.5279	-1.158	0.6085	-0.5494	0.2645	-0.1078	0.0084	0.2251	0.0022	0.2818	-27.8076	69.6108	10.7682
30	4.341	-3.4707	2.1675	6.2036	-2.2954	5.1991	0.2622	0.592	0.4289	-0.5854	-0.3877	-0.6646	-0.3531	0.5295	0.2063	0.277	-0.0421	0.0454	0.3145	0.0608	0.2331	-26.5625	66.3786	-1.6736
31	4.115	-0.4092	-3.3691	1.0662	-0.7764	8.3425	-0.0121	0.294	-0.0565	-0.396	-0.1915	0.0502	-0.4843	-0.8408	0.0432	0.2153	0.0247	-0.0326	0.2761	0.0221	0.1896	-41.6717	66.7919	6.3846

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:18 )	A	1 - 18
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 19:30 )	A	19 - 30
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 31:40 )	A	31 - 40
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 41:50 )	A	41 - 50
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 51:70 )	A	51 - 70
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 71:86 )	A	71 - 86
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 87:100 )	A	87 - 100
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 101:112 )	A	101 - 112
9	X-RAY DIFFRACTION	9	( CHAIN A AND RESID 113:122 )	A	113 - 122
10	X-RAY DIFFRACTION	10	( CHAIN A AND RESID 123:132 )	A	123 - 132
11	X-RAY DIFFRACTION	11	( CHAIN A AND RESID 133:153 )	A	133 - 153
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 1:18 )	B	1 - 18
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 19:30 )	B	19 - 30
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 31:40 )	B	31 - 40
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 41:50 )	B	41 - 50
16	X-RAY DIFFRACTION	16	( CHAIN B AND RESID 51:70 )	B	51 - 70
17	X-RAY DIFFRACTION	17	( CHAIN B AND RESID 71:86 )	B	71 - 86
18	X-RAY DIFFRACTION	18	( CHAIN B AND RESID 87:112 )	B	87 - 112
19	X-RAY DIFFRACTION	19	( CHAIN B AND RESID 113:122 )	B	113 - 122
20	X-RAY DIFFRACTION	20	( CHAIN B AND RESID 123:141 )	B	123 - 141
21	X-RAY DIFFRACTION	21	( CHAIN B AND RESID 142:153 )	B	142 - 153
22	X-RAY DIFFRACTION	22	( CHAIN C AND RESID 1:18 )	C	1 - 18
23	X-RAY DIFFRACTION	23	( CHAIN C AND RESID 19:31 )	C	19 - 31
24	X-RAY DIFFRACTION	24	( CHAIN C AND RESID 32:45 )	C	32 - 45
25	X-RAY DIFFRACTION	25	( CHAIN C AND RESID 46:50 )	C	46 - 50
26	X-RAY DIFFRACTION	26	( CHAIN C AND RESID 51:70 )	C	51 - 70
27	X-RAY DIFFRACTION	27	( CHAIN C AND RESID 71:86 )	C	71 - 86
28	X-RAY DIFFRACTION	28	( CHAIN C AND RESID 87:112 )	C	87 - 112
29	X-RAY DIFFRACTION	29	( CHAIN C AND RESID 113:122 )	C	113 - 122
30	X-RAY DIFFRACTION	30	( CHAIN C AND RESID 123:141 )	C	123 - 141
31	X-RAY DIFFRACTION	31	( CHAIN C AND RESID 142:153 )	C	142 - 153

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