PDB-2qyu: Crystal structure of Salmonella effector protein SopA

ID or keywords:

Entry

Database: PDB / ID: 2qyu

Title

Crystal structure of Salmonella effector protein SopA

Components

Secreted effector protein

Keywords

LIGASE / ubiquitin E3 ligase

Function / homology

Function and homology information

HECT-type E3 ubiquitin transferase / host cell / ubiquitin-protein transferase activity / protein ubiquitination / extracellular region
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Diao, J. / Chen, J.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Crystal structure of SopA, a Salmonella effector protein mimicking a eukaryotic ubiquitin ligase.
Authors: Diao, J. / Zhang, Y. / Huibregtse, J.M. / Zhou, D. / Chen, J.

History

Deposition	Aug 15, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2qyu.cif.gz	257.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2qyu.ent.gz	209.2 KB	Display	PDB format
PDBx/mmJSON format	2qyu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2qyu_validation.pdf.gz	732.8 KB	Display	wwPDB validaton report
Full document	2qyu_full_validation.pdf.gz	744.1 KB	Display
Data in XML	2qyu_validation.xml.gz	25 KB	Display
Data in CIF	2qyu_validation.cif.gz	35.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qy/2qyu ftp://data.pdbj.org/pub/pdb/validation_reports/qy/2qyu	HTTPS FTP

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Related structure data

Related structure data	2qzaC C: citing same article (ref.)
Similar structure data	6qja-d 6w8k-d 6vuq-d 6w8q-d 6w8z-d 3o5d-d 6kzk-d 3gpg-d Search similar-shape structures by Omokage search (details) 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: Secreted effector protein

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	79.720, 79.720, 212.731
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	91
Space group name H-M	P4₁22

Components on special symmetry positions

ID	Model	Components
1	1	A-112- HOH

#1: Protein	Secreted effector protein Mass: 70095.227 Da / Num. of mol.: 1 / Fragment: Residues 163-782 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: SL1344 / Gene: sopA / Plasmid: PET30b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZNR3
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₂₆N₂O₆ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.68 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M sodium potassium phosphate, 0.1M bis-Tris propane (pH6.5), 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.07223 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.07223 Å / Relative weight: 1
Reflection	Resolution: 2.1→50 Å / Num. obs: 37593 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / R_sym value: 0.072 / Net I/σ(I): 14.8
Reflection shell	Resolution: 2.1→2.2 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 2.8 / R_sym value: 0.338 / % possible all: 98.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: SeMet substituted SopA structure model

Resolution: 2.1→50 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.92 / SU B: 12.289 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24916	1887	5 %	RANDOM
R_work	0.20429	-	-	-
obs	0.20644	35698	91.76 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 48.902 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.54 Å²	0 Å²	0 Å²
2-	-	0.54 Å²	0 Å²
3-	-	-	-1.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4832	0	24	134	4990

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4981
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.191	1.945	6791
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.26	5	619
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.905	24.123	228
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.13	15	768
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.976	15	25
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	761
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3827
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	2249
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	3446
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	187
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.22	0.2	66
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.136	0.2	10
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.7	1.5	3171
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	3.414	2	5018
X-RAY DIFFRACTION	r_scbond_it	2.821	3	2027
X-RAY DIFFRACTION	r_scangle_it	4.495	4.5	1773
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.101→2.156 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	113	-
R_work	0.239	2288	-
obs	-	2288	81.28 %

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	130.8034	-36.0892	-28.7269	64.0151	-15.939	16.8446	1.8297	-3.0203	-0.8366	1.4382	-0.6647	5.7982	-0.3775	-2.9243	-1.165	0.642	-0.0852	0.0835	0.559	0.0102	0.4737	-23.359	-44.317	81.6781
2	1.2808	0.0625	-0.2627	1.9613	-0.6867	1.766	-0.0829	-0.2083	-0.0684	0.2145	0.0437	0.1556	-0.0466	-0.2374	0.0391	0.135	0.0286	0.0075	0.2095	-0.0182	0.087	-22.3792	-38.0793	68.3139
3	2.5418	0.3889	-0.2519	2.0209	-0.2322	2.0994	-0.0338	-0.1405	0.1621	0.0931	-0.0159	-0.0377	-0.1042	0.0137	0.0497	0.1997	0.0393	-0.046	0.1425	-0.0277	0.1531	-14.0836	-20.1434	59.9985
4	20.3607	5.1762	-0.427	6.1777	-0.4573	3.1589	0.2189	-0.0678	0.4933	0.1804	-0.1128	0.0892	-0.1641	-0.1995	-0.1061	0.2837	0.0819	-0.0344	0.1125	-0.0255	0.1718	-16.626	-9.8968	55.5278
5	12.1013	-3.7807	-0.2876	6.7804	-0.2723	5.9675	-0.2017	-0.1101	0.9467	0.0523	-0.0158	-0.8084	-0.4063	0.6181	0.2175	0.2544	-0.0197	-0.0559	0.1096	0.0224	0.1958	-6.5293	-12.391	46.2728
6	7.1697	-4.0507	-8.7559	4.8316	5.332	13.0187	0.1379	-0.1048	0.3453	-0.0283	0.0273	-0.1444	-0.4286	0.1662	-0.1651	0.1973	-0.0258	-0.0371	0.0955	0.0006	0.1862	-7.3984	-6.2647	43.8802
7	1.5647	-0.2352	-0.1747	2.3607	-0.5008	2.8334	0.0603	0.0312	0.138	0.0051	-0.011	-0.1661	0.0132	0.0846	-0.0492	0.1457	0.0054	-0.0029	0.1131	0.0225	0.1298	-9.2104	-13.1221	27.2435
8	6.3364	-0.961	0.5132	2.6475	0.9928	2.5699	-0.0104	0.4808	0.4156	-0.4384	-0.0203	-0.0411	-0.112	-0.0141	0.0308	0.2309	-0.0124	0.0248	0.1656	0.0173	0.0966	-8.9705	-17.1609	13.9495
9	4.4337	-2.5084	3.7498	5.0295	-4.1924	8.8558	0.084	0.5663	0.1186	-0.5501	-0.3175	-0.6193	0.2496	0.5014	0.2335	0.144	0.0353	0.1328	0.1678	0.0028	0.1374	2.8296	-20.4718	11.137
10	3.9018	-5.1229	2.0993	29.7721	-6.9876	2.4606	-0.0228	0.206	0.0518	-0.6004	-0.0392	0.2006	0.0431	-0.2032	0.062	0.1618	0.0066	0.098	0.1777	0.0124	0.0826	7.6383	-40.1938	23.3884
11	5.5236	-1.2431	-2.1168	20.6278	5.955	8.7386	0.1178	0.6698	0.1329	-0.3258	-0.3989	0.2373	0.1439	-0.8515	0.2811	0.1396	0.0058	0.0549	0.3218	0.0448	0.1314	0.2425	-45.8661	30.1505
12	3.2007	-0.7413	-1.2469	2.0342	0.436	1.6518	-0.1882	-0.3042	-0.0987	-0.0139	0.0773	-0.1566	0.1915	0.2185	0.1109	0.1746	0.0053	0.0432	0.1622	0.0003	0.1452	11.211	-52.2932	34.1664
13	7.5745	4.2082	1.4468	8.98	0.3316	8.3407	-0.3527	0.76	0.0442	-0.6331	0.4012	-0.5389	-0.3379	0.4842	-0.0485	0.17	-0.0516	0.1021	0.1723	0.0562	0.2432	21.6657	-38.2266	22.7333
14	6.5273	1.5011	-1.4727	2.8511	-1.3624	2.0728	0.0754	-0.5246	0.0564	0.2266	-0.1351	-0.1734	-0.0929	0.1767	0.0596	0.1835	-0.0276	-0.0072	0.154	-0.0187	0.1732	14.6804	-42.7677	38.0189
15	21.9199	9.8269	-5.7795	17.4789	-5.7433	6.4823	-0.1147	-1.6699	0.3215	0.9915	-0.3204	-0.5288	-0.2821	0.7521	0.4352	0.0712	-0.0525	-0.1925	0.2338	-0.101	0.1047	23.4124	-39.5869	44.082
16	21.7563	13.1864	-19.6791	28.0197	7.02	35.7258	0.2002	-1.4953	-2.1127	-2.4981	2.3677	5.8136	1.602	2.2969	-2.568	0.5598	0.0001	0.0039	0.558	0.0017	0.5601	12.9397	-46.0553	51.4987
17	13.7281	10.9763	-8.2844	31.1902	-21.7713	15.236	-0.0687	-0.8986	1.3334	0.7633	-0.0066	0.5291	-0.9018	0.2609	0.0753	0.3001	0.0012	-0.0392	0.1291	-0.2492	0.2511	16.2101	-30.9977	40.8251
18	15.1502	2.6121	-1.2534	1.6985	-0.9883	2.911	0.5311	0.2007	1.225	0.6386	-0.1477	-0.2185	-0.7545	0.0142	-0.3833	0.1998	0.0026	-0.0024	-0.0343	0.0397	0.3705	12.7608	-30.6514	32.0054

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	163 - 169	8 - 14
2	X-RAY DIFFRACTION	2	A	A	170 - 279	15 - 124
3	X-RAY DIFFRACTION	3	A	A	280 - 364	125 - 209
4	X-RAY DIFFRACTION	4	A	A	365 - 385	210 - 230
5	X-RAY DIFFRACTION	5	A	A	386 - 409	231 - 254
6	X-RAY DIFFRACTION	6	A	A	410 - 428	255 - 273
7	X-RAY DIFFRACTION	7	A	A	429 - 509	274 - 354
8	X-RAY DIFFRACTION	8	A	A	510 - 558	355 - 403
9	X-RAY DIFFRACTION	9	A	A	559 - 596	404 - 441
10	X-RAY DIFFRACTION	10	A	A	597 - 614	442 - 459
11	X-RAY DIFFRACTION	11	A	A	615 - 633	460 - 478
12	X-RAY DIFFRACTION	12	A	A	634 - 666	479 - 511
13	X-RAY DIFFRACTION	13	A	A	667 - 684	512 - 529
14	X-RAY DIFFRACTION	14	A	A	685 - 729	530 - 574
15	X-RAY DIFFRACTION	15	A	A	730 - 745	575 - 590
16	X-RAY DIFFRACTION	16	A	A	746 - 756	591 - 601
17	X-RAY DIFFRACTION	17	A	A	757 - 767	602 - 612
18	X-RAY DIFFRACTION	18	A	A	768 - 782	613 - 627

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