PDB-4fml: Catalytic domain of VahC from Aeromonas hydrophila

ID or keywords:

Entry

Database: PDB / ID: 4fml

Title

Catalytic domain of VahC from Aeromonas hydrophila

Components

VsdC

Keywords

TRANSFERASE

Function / homology

Function and homology information

toxin activity / extracellular region
Similarity search - Function

Biological species

Aeromonas hydrophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Ravulapalli, R. / Kimber, M.S. / Merrill, A.R.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Characterization of an actin-targeting ADP-ribosyltransferase from Aeromonas hydrophila.
Authors: Shniffer, A. / Visschedyk, D.D. / Ravulapalli, R. / Suarez, G. / Turgeon, Z.J. / Petrie, A.A. / Chopra, A.K. / Merrill, A.R.

History

Deposition	Jun 18, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 19, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 2, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.3	Feb 28, 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	4fml.cif.gz	338.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4fml.ent.gz	285.4 KB	Display	PDB format
PDBx/mmJSON format	4fml.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/fm/4fml ftp://data.pdbj.org/pub/pdb/validation_reports/fm/4fml	HTTPS FTP

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Related structure data

Related structure data	3nts
Similar structure data	6zje-d 3kln-3 1zd8-d 5nri-1 2ykd-d 4gl6-1 3wwt-d 1npy-4 2hz0-2 5jp3-2 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

3nts

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: VsdC

B: VsdC

C: VsdC

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

1

A: VsdC

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

2

B: VsdC

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

3

C: VsdC

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

Unit cell

Length a, b, c (Å)	91.100, 91.100, 303.370
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	B-302- HOH

#1: Protein	VsdC Mass: 24741.781 Da / Num. of mol.: 3 / Fragment: UNP residues 67-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: VahC, vsdC / Production host: Escherichia coli (E. coli) / References: UniProt: Q49TP5
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.48 Å³/Da / Density % sol: 50.42 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG 3350, 0.2 M NaCl, 0.1M Hepes, 5% glycerol, 2 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
Detector	Type: RAYONIX MX-300 / Detector: CCD / Date: Aug 21, 2011
Radiation	Monochromator: Double Crystal Monochromator (ACCEL DCM) with an indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 1.93→45.55 Å / Num. all: 57036 / Num. obs: 57036 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / R_merge(I) obs: 0.08 / R_sym value: 0.085 / Net I/σ(I): 31.2
Reflection shell	Resolution: 1.93→1.98 Å / R_merge(I) obs: 0.492 / Mean I/σ(I) obs: 3.67 / R_sym value: 1.2 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
MxDC		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
AutoProcess	(XDS	data reduction
BEST		data reduction
pointless	based automatic processing script)	data scaling
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→45.55 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 19.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2173	2852	5 %
R_work	0.1912	-	-
obs	0.1925	57036	99.87 %
all	-	57036	-

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-	0.3798 Å²	0 Å²	-0 Å²
2-	-	0.3798 Å²	0 Å²
3-	-	-	-0.7597 Å²

Refinement step

Cycle: LAST / Resolution: 1.93→45.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4360	0	0	412	4772

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.021	4462
X-RAY DIFFRACTION	f_angle_d	1.5	6041
X-RAY DIFFRACTION	f_dihedral_angle_d	14.009	1683
X-RAY DIFFRACTION	f_chiral_restr	0.132	687
X-RAY DIFFRACTION	f_plane_restr	0.008	784

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 (%)
1.93-1.9633	0.3143	137	0.2597	2614	X-RAY DIFFRACTION	100
1.9633-1.999	0.2634	141	0.2557	2674	X-RAY DIFFRACTION	100
1.999-2.0375	0.261	139	0.2455	2636	X-RAY DIFFRACTION	100
2.0375-2.0791	0.2531	140	0.2274	2662	X-RAY DIFFRACTION	100
2.0791-2.1243	0.2499	139	0.2136	2638	X-RAY DIFFRACTION	100
2.1243-2.1737	0.2318	140	0.2101	2671	X-RAY DIFFRACTION	100
2.1737-2.228	0.2591	140	0.208	2648	X-RAY DIFFRACTION	100
2.228-2.2883	0.2289	140	0.2021	2663	X-RAY DIFFRACTION	100
2.2883-2.3556	0.2175	140	0.197	2674	X-RAY DIFFRACTION	100
2.3556-2.4316	0.1982	142	0.19	2681	X-RAY DIFFRACTION	100
2.4316-2.5185	0.2491	140	0.1911	2677	X-RAY DIFFRACTION	100
2.5185-2.6194	0.209	142	0.1871	2696	X-RAY DIFFRACTION	100
2.6194-2.7386	0.2204	142	0.1924	2700	X-RAY DIFFRACTION	100
2.7386-2.8829	0.2375	142	0.1913	2698	X-RAY DIFFRACTION	100
2.8829-3.0635	0.2153	144	0.1933	2721	X-RAY DIFFRACTION	100
3.0635-3.3	0.1818	144	0.1876	2743	X-RAY DIFFRACTION	100
3.3-3.6319	0.2165	144	0.1746	2742	X-RAY DIFFRACTION	100
3.6319-4.1572	0.2079	148	0.1654	2800	X-RAY DIFFRACTION	100
4.1572-5.2364	0.1744	147	0.1588	2806	X-RAY DIFFRACTION	100
5.2364-45.5627	0.2388	161	0.2209	3040	X-RAY DIFFRACTION	100

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	0.8255	0.7604	0.3848	0.9884	0.2074	2.4383	-0.0312	-0.014	1.6443	-1.0119	-0.0991	-0.6825	-0.9594	-0.3522	0.0527	0.6848	0.0623	0.2007	0.2158	0.004	1.1683	26.8307	38.8488	-38.8204
2	2.7441	0.3116	-0.723	1.839	-0.4661	2.803	0.0616	0.1438	0.293	-0.111	-0.1132	-0.2121	-0.0386	0.237	0.026	0.2282	0.0379	0.0524	0.2266	0.0524	0.2604	40.8673	17.0428	-43.6281
3	5.4158	2.4709	1.1307	5.5746	0.5724	5.887	0.1352	-0.1608	0.2545	0.4409	-0.0597	0.0397	-0.0806	-0.0473	-0.0777	0.1727	0.0716	0.0094	0.1938	-0.0125	0.2117	4.8679	46.8497	-24.6601
4	2.9811	-0.7525	2.0285	2.51	-0.3815	3.7317	0.013	0.2011	-0.2114	-0.1244	0.001	0.0355	0.1803	0.0317	0.013	0.2169	0.0205	0.0328	0.2287	-0.029	0.2015	2.4891	45.321	-34.8552
5	2.2359	-1.0876	-0.3379	1.7765	-1.4072	2.054	-0.0388	0.0102	-0.356	-0.2745	0.1492	0.4931	0.2019	-0.4643	-0.0582	0.2376	0.0164	-0.0651	0.3129	0.0159	0.2947	9.236	23.8671	-22.4048
6	5.2005	0.1921	-0.0868	2.7863	-1.0562	2.2153	0.0136	-0.3564	-0.0995	0.3583	0.1284	0.3801	-0.2426	-0.3687	-0.1525	0.2361	0.0748	-0.0037	0.2802	-0.018	0.2225	10.5841	30.2101	-16.5781
7	3.8131	-3.0483	-4.4343	7.0245	2.6998	5.9873	-0.0335	-0.6319	0.0033	0.8888	0.389	0.4406	-0.503	-0.3153	-0.1848	0.4425	0.138	0.028	0.4335	0.0201	0.334	7.7834	38.629	-15.8015
8	4.7061	0.8108	-2.2944	6.1419	-2.1758	8.6118	-0.0143	-0.4295	-0.8468	0.1138	0.0566	0.3363	0.7649	-0.1559	0.0532	0.2875	-0.0321	-0.0704	0.3337	0.0581	0.4326	11.5305	16.1805	-15.0977
9	6.027	-0.2577	0.8109	3.5034	2.8562	2.5277	0.1754	-0.5903	-0.331	0.1969	0.045	1.0354	0.5107	-0.7825	-0.1686	0.2833	-0.0446	-0.062	0.4703	0.1527	0.5214	6.2888	17.5272	-16.0711
10	6.0427	-2.9178	0.4919	5.2353	0.6109	1.8486	-0.0336	-0.4012	-0.5184	0.3953	-0.4757	1.6533	0.0955	-0.3069	0.3987	1.4545	-0.1598	-0.3563	1.0271	-0.1312	1.5842	25.3663	-8.2014	-67.3617
11	1.9405	-1.954	-1.5003	6.9493	1.1029	1.1951	-0.31	-0.4064	0.2641	0.0587	0.1866	-0.2525	-0.3934	0.1156	0.1771	1.6872	0.1117	-0.4219	1.2204	-0.4626	1.6236	36.1749	-13.4882	-72.818
12	1.2532	-2.7265	-2.7902	8.3795	4.0013	7.9624	1.1938	1.4993	-2.5235	-0.3991	-0.126	-0.1401	0.5858	1.1043	-1.1508	1.4266	0.3018	-0.4854	1.2786	-0.5497	2.0129	33.5917	-15.8183	-80.0186
13	8.4676	-3.2599	-5.7788	2.6546	2.4117	3.9684	-0.5637	1.1296	-0.5189	-2.767	-1.588	3.4639	-1.3773	-1.4802	2.1861	1.744	0.1697	-0.605	0.8971	-0.256	1.8362	21.5317	-11.2473	-82.1785
14	9.2158	1.2672	4.393	7.2766	2.2259	5.0103	0.6723	-0.0907	-1.0187	-1.2269	-0.3283	0.9421	0.4013	-0.3054	-0.1842	1.0978	0.0525	-0.1044	0.8372	-0.1194	1.0613	36.6284	-0.6083	-63.0083
15	2.0005	-0.0115	-2.2945	2.0078	1.9903	8.217	0.0353	2.0301	-0.0907	-1.3589	1.5674	-2.1809	-1.0096	1.4404	-1.4894	1.5821	-0.2552	0.2897	1.3531	-0.3707	1.1863	54.6164	2.0916	-71.8634
16	6.1093	1.9218	0.227	7.6181	2.2866	7.6477	-0.6417	0.5082	-0.2651	-0.8575	1.3367	-0.1899	1.3892	0.3818	-0.7001	1.3408	-0.0992	-0.0009	0.8077	-0.1712	1.073	42.0155	-4.9058	-63.3146
17	7.7488	2.0418	0.1103	3.7985	-0.5691	4.0006	-0.3941	-0.1558	-0.6933	0.059	0.1953	-0.5729	1.1231	0.2276	0.2577	1.7504	0.1045	0.1197	1.1822	-0.0857	1.5529	52.0922	-11.8902	-57.5621
18	7.4629	3.1113	0.6951	2.7992	-2.0015	6.581	-0.6908	0.1362	0.3793	0.2404	0.6276	-0.0284	0.5034	-0.062	0.3098	0.9312	0.0641	0.179	0.7648	-0.0564	1.2081	44.3323	2.4283	-60.9837
19	8.9999	3.2289	-0.2312	3.9558	4.896	8.8903	0.1217	1.0141	-0.1872	-0.6224	-0.4086	-0.4752	1.5527	0.8084	0.2519	1.4371	0.1788	0.158	0.8881	-0.0036	1.0346	38.9066	-3.5229	-63.8759
20	6.1417	-3.4323	1.6822	7.1369	-1.5058	4.1121	-0.286	-0.4874	0.6663	-0.4561	0.4838	-1.352	0.4252	1.4372	0.0157	0.9704	0.1609	0.0886	1.6115	-0.1058	1.2013	58.2908	2.5751	-63.8361
21	9.3531	0.1522	2.4107	6.5055	0.4685	3.8947	0.4456	-0.1864	-0.5568	-1.2496	-0.5428	-0.9319	0.7515	1.0237	0.0487	1.3067	0.321	-0.1449	1.0964	-0.1198	1.4599	58.0697	-1.7932	-52.0504
22	9.2518	-2.8619	0.8693	2.0081	0.9181	4.5532	-0.3339	0.3503	0.1814	0.3249	0.5218	-1.4764	0.8609	0.9248	-0.1204	1.1478	0.1609	0.0417	1.0052	-0.0502	1.1612	56.5332	-2.9616	-62.0277

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 63 through 136 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 137 through 266 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 65 through 89 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 90 through 136 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 137 through 173 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 174 through 207 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 208 through 221 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 222 through 247 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 254 through 266 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 68 through 80 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 81 through 88 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 89 through 105 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 106 through 125 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 126 through 151 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 164 through 173 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 174 through 183 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 184 through 188 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 189 through 204 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 213 through 222 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 223 through 236 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 237 through 246 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 256 through 266 )

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