PDB-3let: Crystal Structure of Fic domain containing AMPylator, VopS

ID or keywords:

Entry

Database: PDB / ID: 3let

Title

Crystal Structure of Fic domain containing AMPylator, VopS

Components

Adenosine monophosphate-protein transferase vopS

Keywords

TRANSFERASE / AMPylation / Fic domain / Vibrio / Type III / effector / T3SS / Nucleotidyltransferase / Virulence

Function / homology

Function and homology information

symbiont-mediated perturbation of host small GTPase-mediated signal transduction / AMPylase activity / protein adenylyltransferase / small GTPase binding / extracellular region / ATP binding
Similarity search - Function

Biological species

Vibrio parahaemolyticus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.802 Å

Authors

Luong, P.H. / Kinch, L.N. / Brautigam, C.A. / Grishin, N.V. / Tomchick, D.R. / Orth, K.

Citation

Journal: To be Published
Title: Structural and Kinetic Analysis of VopS with Fic Domain Supports a Direct Transfer Mechanism for AMPylation
Authors: Luong, P.H. / Kinch, L.N. / Brautigam, C.A. / Grishin, N.V. / Tomchick, D.R. / Orth, K.

History

Deposition	Jan 15, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 21, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4	Feb 21, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3let.cif.gz	347.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3let.ent.gz	291.9 KB	Display	PDB format
PDBx/mmJSON format	3let.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3let_validation.pdf.gz	436 KB	Display	wwPDB validaton report
Full document	3let_full_validation.pdf.gz	439.9 KB	Display
Data in XML	3let_validation.xml.gz	33.2 KB	Display
Data in CIF	3let_validation.cif.gz	46.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/le/3let ftp://data.pdbj.org/pub/pdb/validation_reports/le/3let	HTTPS FTP

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Related structure data

Similar structure data	4qpl-1 4kzg-8 5wbs-3 4m6d-1 4qpl-2 5he8-1 2q7a-d 2bp5-d 5a5c-3 1bjj-9 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 - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Adenosine monophosphate-protein transferase vopS

B: Adenosine monophosphate-protein transferase vopS

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

1

A: Adenosine monophosphate-protein transferase vopS

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

2

B: Adenosine monophosphate-protein transferase vopS

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

Unit cell

Length a, b, c (Å)	66.669, 62.325, 75.762
Angle α, β, γ (deg.)	90.00, 91.31, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Adenosine monophosphate-protein transferase vopS / AMPylator vopS / Vibrio outer protein S Mass: 33973.281 Da / Num. of mol.: 2 / Fragment: Residues 75-387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: POR1 / Gene: vopS, VP 1686, VP1686 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 References: UniProt: Q87P32, nicotinamide-nucleotide adenylyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 514 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Adenosine monophosphate-protein transferase vopS / AMPylator vopS / Vibrio outer protein S

Mass: 33973.281 Da / Num. of mol.: 2 / Fragment: Residues 75-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio parahaemolyticus (bacteria) / Strain: POR1 / Gene: vopS, VP 1686, VP1686 / Plasmid: pGEXTEV / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q87P32, nicotinamide-nucleotide adenylyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.32 Å³/Da / Density % sol: 46.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 21% PEG 3350, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97918 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 18, 2008

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. all: 57468 / Num. obs: 57468 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / B_iso Wilson estimate: 22.9 Å² / R_merge(I) obs: 0.088 / Net I/σ(I): 7

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	% possible all
1.8-1.83	3.6	0.84	100
1.83-1.86	3.9	0.762	100
1.86-1.9	4	0.627	100
1.9-1.94	4.1	0.535	100
1.94-1.98	4.1	0.43	100
1.98-2.03	4.1	0.336	100
2.03-2.08	4.2	0.256	100
2.08-2.13	4.2	0.203	100
2.13-2.2	4.1	0.167	100
2.2-2.27	4.2	0.154	100
2.27-2.35	4.2	0.13	100
2.35-2.44	4.1	0.11	100
2.44-2.55	4.2	0.097	100
2.55-2.69	4.1	0.082	100
2.69-2.86	4.1	0.074	100
2.86-3.08	4.1	0.066	100
3.08-3.39	4.1	0.063	100
3.39-3.88	4	0.052	100
3.88-4.88	3.9	0.047	100
4.88-50	4	0.051	98.9

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction
HKL-3000		data collection
HKL-3000		data reduction
SHELXS		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.802→48.126 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.29 / Isotropic thermal model: isotropic / σ(F): 1.33 / Phase error: 23.55 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2239	2909	5.07 %
R_work	0.1747	-	-
obs	0.1772	57380	99.7 %
all	-	57381	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 42.477 Å² / k_sol: 0.384 e/Å³

Displacement parameters

B_iso mean: 33.371 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.657 Å²	0 Å²	1.421 Å²
2-	-	3.094 Å²	-0 Å²
3-	-	-	-3.751 Å²

Refine analyze

Luzzati coordinate error obs: 0.28 Å

Refinement step

Cycle: LAST / Resolution: 1.802→48.126 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4642	0	0	514	5156

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	9289
X-RAY DIFFRACTION	f_angle_d	0.887	16793
X-RAY DIFFRACTION	f_dihedral_angle_d	14.412	2343
X-RAY DIFFRACTION	f_chiral_restr	0.073	702
X-RAY DIFFRACTION	f_plane_restr	0.004	1515

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 (%)
1.802-1.8664	0.315	263	0.2468	5363	X-RAY DIFFRACTION	99
1.8664-1.9411	0.2759	280	0.2147	5453	X-RAY DIFFRACTION	100
1.9411-2.0295	0.2602	295	0.1979	5411	X-RAY DIFFRACTION	100
2.0295-2.1365	0.2481	286	0.176	5426	X-RAY DIFFRACTION	100
2.1365-2.2703	0.2089	274	0.1567	5437	X-RAY DIFFRACTION	100
2.2703-2.4456	0.2132	310	0.1565	5445	X-RAY DIFFRACTION	100
2.4456-2.6917	0.213	295	0.1577	5447	X-RAY DIFFRACTION	100
2.6917-3.0811	0.2433	285	0.1753	5466	X-RAY DIFFRACTION	100
3.0811-3.8817	0.2204	297	0.1669	5489	X-RAY DIFFRACTION	100
3.8817-48.1436	0.1881	324	0.1662	5534	X-RAY DIFFRACTION	99

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	1.5995	-0.9095	1.2334	1.5329	-0.9629	0.9754	0.1138	-0.0624	-0.4905	-0.3097	0.1738	0.5456	0.337	-0.138	-0.3274	0.2748	-0.0427	-0.0778	0.2127	0.026	0.2877	27.5717	20.2447	34.0514
2	0.3907	0.3638	-0.0264	0.8088	0.3788	0.2997	0.015	0.2247	0.0081	-0.016	0.0032	0.1549	0.198	0.221	-0.0072	0.1905	0.0396	-0.0033	0.2369	0.0155	0.1647	34.762	27.2037	29.1545
3	0.393	-0.1962	0.4534	0.1571	-0.2412	1.3693	0.01	0.121	0.0156	0.0124	-0.003	0.007	-0.0845	0.0617	-0.01	0.0977	0.0162	-0.0088	0.1436	-0.0015	0.1113	36.7225	26.5547	44.3491
4	1.5734	-0.1333	1.5375	0.2109	0.527	3.1848	-0.1789	0.1142	0.117	-0.0325	0.0989	-0.0068	-0.2958	0.3833	0.0695	0.1202	-0.0241	-0.0289	0.1591	0.0055	0.1329	46.2179	31.9582	55.1425
5	0.928	1.078	-0.572	1.641	0.0928	1.537	0.1028	-0.1736	0.2208	0.2028	0.139	0.1385	-0.0958	0.0179	-0.1408	0.1619	0.0186	0.0049	0.1053	-0.0305	0.1341	38.4593	40.2293	90.5242
6	1.1073	-0.8677	-0.4703	-0.169	-0.2426	2.6429	-0.1056	-0.1441	0.11	0.041	0.1029	0.0044	0.1877	-0.2693	0.0239	0.1546	-0.0269	0.0277	0.1324	-0.0202	0.1498	27.4716	33.8462	83.5865
7	0.9742	-0.0677	-0.4887	0.4959	0.6979	1.198	0.1462	0.0008	-0.0395	-0.0109	-0.0296	0.0567	0.0457	-0.2465	-0.069	0.136	-0.0153	0.0264	0.116	-0.0022	0.1307	30.0668	30.5964	71.9265
8	0.1428	0.1357	0.1989	0.2304	0.7231	0.5785	-0.0282	-0.0412	0.1223	-0.0752	0.0036	-0.0939	-0.1241	-0.0168	0.0106	0.0873	0.0041	-0.0117	0.0943	-0.0083	0.1188	41.6842	30.2931	63.1234
9	0.4843	0.1838	0.1806	0.5572	0.6298	0.9263	-0.0115	-0.0596	-0.1097	0.125	-0.0133	-0.0698	0.0735	0.0379	0.0118	0.1097	0.0238	-0.0253	0.1077	0.0015	0.1174	40.9734	30.388	79.33
10	0.8643	0.4488	0.7619	0.4483	-1.2157	6.656	0.0092	0.1106	0.0412	0.1238	0.0633	0.1838	-0.6254	0.3249	0.0386	0.1945	-0.0409	-0.0281	0.1571	-0.0142	0.1427	49.829	38.683	77.6828
11	1.8577	1.7686	-1.6795	-1.8848	-1.3785	5.2315	0.1028	0.1155	-0.2957	1.2008	-0.4671	0.4297	-0.6813	0.0595	0.2754	0.6243	0.013	0.0154	0.3075	-0.0028	0.4087	93.1911	14.7069	77.8788
12	2.3134	0.857	1.0595	1.7721	0.607	1.6065	0.4443	0.0419	-0.7051	0.0337	-0.1352	-0.5139	0.2058	0.1932	-0.2432	0.1515	0.0074	-0.0386	0.1426	0.0218	0.2689	81.1504	19.999	71.3788
13	2.048	0.2294	0.5443	0.7835	-0.0669	0.1563	-0.0094	-0.1509	-0.1388	0.0009	0.1883	-0.0118	0.0059	-0.031	-0.1332	0.1586	-0.0309	-0.0011	0.1719	-0.0067	0.1465	73.8545	26.9445	76.6981
14	-0.0102	-0.051	-0.1499	0.4325	0.2324	0.562	0.0306	0.0236	0.0138	-0.0506	-0.0005	-0.1008	0.0066	-0.1027	-0.0172	0.1252	-0.0291	-0.0224	0.1531	0.0032	0.1365	71.9657	26.6297	61.6161
15	1.5524	0.1979	0.2405	0.3204	-0.6871	1.9966	-0.1599	0.1271	0.0646	-0.0144	0.1526	-0.0185	-0.0842	-0.2871	0.0132	0.0898	-0.0136	-0.0108	0.1793	0.0024	0.0925	63.1935	31.4606	53.3814
16	0.397	-0.5944	-0.2169	1.7975	0.4515	2.308	0.1948	0.0597	0.1426	-0.344	-0.0575	-0.0537	-0.2069	-0.5187	-0.106	0.1847	0.0334	-0.026	0.1902	0.0124	0.1011	67.1436	38.3248	16.283
17	1.4545	-0.9432	-0.4639	1.8605	0.1702	0.5886	-0.0521	0.1356	0.2527	0.0611	0.1839	-0.1423	0.0806	0.03	-0.0951	0.1472	0.0254	0.003	0.1535	0.0221	0.1807	80.9363	34.0044	22.2471
18	0.8182	-0.938	-1.1623	2.2908	-1.1967	2.5481	-0.2396	-0.2314	-0.1017	0.1488	0.1704	-0.0478	0.3584	0.2838	0.0861	0.1661	0.0353	-0.0052	0.1522	0.0417	0.118	78.0875	29.0567	32.9934
19	0.5586	0.5913	-1.1382	1.167	-1.2669	2.0004	-0.0683	0.1636	0.0533	-0.0574	0.0021	0.0764	0.2068	-0.0754	0.0349	0.1364	-0.0122	-0.0112	0.1961	0.0326	0.1272	68.6195	33.2353	43.7317
20	0.2409	0.0467	-1.6418	3.9045	2.4566	-4.212	-0.2745	0.3355	-0.3392	-0.9524	-0.0851	0.1539	0.0048	-0.2357	0.2779	0.5761	-0.067	0.1273	0.3034	-0.0692	0.1665	63.7201	17.9651	27.5899
21	0.63	0.2173	-0.0425	0.4309	-0.0982	2.6561	0.0106	-0.1111	0.009	-0.0163	-0.0344	0.0312	0.0745	-0.5398	0.0132	0.102	-0.0168	-0.0085	0.205	-0.0008	0.0946	66.3012	32.7199	27.1877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resid 86:109
2	X-RAY DIFFRACTION	2	chain A and resid 110:126
3	X-RAY DIFFRACTION	3	chain A and resid 127:164
4	X-RAY DIFFRACTION	4	chain A and resid 165:225
5	X-RAY DIFFRACTION	5	chain A and resid 226:255
6	X-RAY DIFFRACTION	6	chain A and resid 256:275
7	X-RAY DIFFRACTION	7	chain A and resid 276:295
8	X-RAY DIFFRACTION	8	chain A and resid 296:329
9	X-RAY DIFFRACTION	9	chain A and resid 330:374
10	X-RAY DIFFRACTION	10	chain A and resid 375:387
11	X-RAY DIFFRACTION	11	chain B and resid 80:85
12	X-RAY DIFFRACTION	12	chain B and resid 86:109
13	X-RAY DIFFRACTION	13	chain B and resid 110:126
14	X-RAY DIFFRACTION	14	chain B and resid 127:164
15	X-RAY DIFFRACTION	15	chain B and resid 165:220
16	X-RAY DIFFRACTION	16	chain B and resid 221:255
17	X-RAY DIFFRACTION	17	chain B and resid 256:275
18	X-RAY DIFFRACTION	18	chain B and resid 276:292
19	X-RAY DIFFRACTION	19	chain B and resid 293:326
20	X-RAY DIFFRACTION	20	chain B and resid 327:335
21	X-RAY DIFFRACTION	21	chain B and resid 336:386

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