PDB-6ih1: Crystal structure of a standalone versatile EAL protein from Vibr...

ID or keywords:

Entry

Database: PDB / ID: 6ih1

Title

Crystal structure of a standalone versatile EAL protein from Vibrio cholerae O395 - c-di-GMP bound form

Components

cyclic di nucleotide phoshodiesterase

Keywords

HYDROLASE / cyclic dinucleotide phosphodiesterase / nucleotide binding

Function / homology

Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain / EAL domain profile. / nucleotide binding / metal ion binding / Chem-C2E / EAL domain-containing protein

Function and homology information

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 1.95 Å

Authors

Yadav, M. / Pal, K. / Sen, U.

Citation

Journal: Biochem.J. / Year: 2019
Title: Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication.
Authors: Yadav, M. / Pal, K. / Sen, U.

History

Deposition	Sep 28, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 2, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2020	Group: Database references / Structure summary / Category: chem_comp / citation / citation_author Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2	Mar 27, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6ih1.cif.gz	416.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ih1.ent.gz	342.3 KB	Display	PDB format
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Validation report

Summary document	6ih1_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	6ih1_full_validation.pdf.gz	1.6 MB	Display
Data in XML	6ih1_validation.xml.gz	47 KB	Display
Data in CIF	6ih1_validation.cif.gz	63.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ih/6ih1 ftp://data.pdbj.org/pub/pdb/validation_reports/ih/6ih1	HTTPS FTP

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Related structure data

Related structure data	6ifqC 6ih7C 6ij2C C: citing same article (ref.)
Similar structure data	6ij2-1 6k6t-1 6s8s-d 3t1f-d 4nk5-1 4x6f-d 5gkp-d 5j1a-d 4qu3-d 2gju-3 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
Related items in Molecule of the Month	#130 - Oct 2010 Riboswitches similarity (1)

Deposited unit

A: cyclic di nucleotide phoshodiesterase

B: cyclic di nucleotide phoshodiesterase

C: cyclic di nucleotide phoshodiesterase

D: cyclic di nucleotide phoshodiesterase

hetero molecules

119 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: cyclic di nucleotide phoshodiesterase

C: cyclic di nucleotide phoshodiesterase

hetero molecules

defined by author&software
Evidence: gel filtration
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: cyclic di nucleotide phoshodiesterase

D: cyclic di nucleotide phoshodiesterase

hetero molecules

defined by author&software
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	73.500, 42.630, 156.340
Angle α, β, γ (deg.)	90.000, 94.420, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	chain B
3	1	chain C
4	1	chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Auth seq-ID: 21 - 257 / Label seq-ID: 21 - 257

Dom-ID	Selection details	Auth asym-ID	Label asym-ID
1	chain A	A	A
2	chain B	B	B
3	chain C	C	C
4	chain D	D	D

#1: Protein	cyclic di nucleotide phoshodiesterase Mass: 29041.152 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria) Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: VC0395_A1247 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0H3AJ04, cyclic-guanylate-specific phosphodiesterase
#2: Chemical	ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate Mass: 690.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂
#3: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.11 Å³/Da / Density % sol: 41.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, ammonium acetate, sodium citrate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54179 Å

Detector

Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 15, 2016

Radiation

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

Radiation wavelength

Wavelength: 1.54179 Å / Relative weight: 1

Reflection

Resolution: 1.95→41.12 Å / Num. obs: 68489 / % possible obs: 96.5 % / Redundancy: 1.8 % / B_iso Wilson estimate: 27.45 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.052 / R_pim(I) all: 0.049 / R_rim(I) all: 0.072 / Net I/σ(I): 6 / Num. measured all: 126224 / Scaling rejects: 6

Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)	R_merge(I) obs	Num. measured all	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
1.95-2	0.327	8135	4400	0.763	0.315	0.454	1.7	93.8
9.15-41.12	0.024	1215	663	0.997	0.024	0.034	11.3	90.1

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
Aimless	0.3.11	data scaling
PDB_EXTRACT	3.24	data extraction
MOSFLM		data reduction
PHASER		phasing

Refinement

Resolution: 1.95→40.923 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.13 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2217	3317	4.85 %
R_work	0.1833	65074	-
obs	0.1852	68391	95.87 %

Solvent computation

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

Displacement parameters

B_iso max: 221.1 Å² / B_iso mean: 50.8677 Å² / B_iso min: 12.74 Å²

Refinement step

Cycle: final / Resolution: 1.95→40.923 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7580	0	192	562	8334
B_iso mean	-	-	39.69	47.26	-
Num. residues	-	-	-	-	948

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	7990
X-RAY DIFFRACTION	f_angle_d	1.054	10780
X-RAY DIFFRACTION	f_chiral_restr	0.059	1180
X-RAY DIFFRACTION	f_plane_restr	0.006	1372
X-RAY DIFFRACTION	f_dihedral_angle_d	16.625	4672

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4658	X-RAY DIFFRACTION	17.551	TORSIONAL
1	2	B	4658	X-RAY DIFFRACTION	17.551	TORSIONAL
1	3	C	4658	X-RAY DIFFRACTION	17.551	TORSIONAL
1	4	D	4658	X-RAY DIFFRACTION	17.551	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 24

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.95-1.9779	0.333	135	0.2729	2618	2753	93
1.9779-2.0074	0.2936	131	0.2711	2611	2742	94
2.0074-2.0388	0.2774	127	0.2628	2662	2789	94
2.0388-2.0722	0.2981	129	0.2397	2636	2765	94
2.0722-2.1079	0.2862	132	0.2289	2647	2779	94
2.1079-2.1462	0.2775	127	0.2176	2653	2780	94
2.1462-2.1875	0.2486	130	0.2016	2629	2759	95
2.1875-2.2322	0.2345	122	0.1903	2725	2847	95
2.2322-2.2807	0.2119	134	0.1868	2647	2781	96
2.2807-2.3337	0.2138	141	0.1939	2651	2792	95
2.3337-2.3921	0.2598	140	0.1917	2721	2861	96
2.3921-2.4568	0.241	133	0.1843	2703	2836	96
2.4568-2.5291	0.2268	127	0.1843	2717	2844	96
2.5291-2.6107	0.2146	153	0.1908	2702	2855	96
2.6107-2.704	0.2301	154	0.1911	2710	2864	97
2.704-2.8122	0.2431	122	0.1915	2774	2896	97
2.8122-2.9402	0.2416	132	0.1759	2755	2887	97
2.9402-3.0951	0.2614	122	0.1818	2776	2898	98
3.0951-3.289	0.2302	146	0.1649	2785	2931	98
3.289-3.5428	0.1817	137	0.1561	2815	2952	98
3.5428-3.899	0.2032	150	0.161	2793	2943	98
3.899-4.4626	0.1645	146	0.1453	2801	2947	99
4.4626-5.6201	0.2103	155	0.1711	2817	2972	98
5.6201-40.9324	0.2183	192	0.2099	2726	2918	93

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	2.5178	0.0245	1.2796	3.5831	-0.3947	2.4674	-0.0505	-1.2688	-0.1968	0.8966	0.0216	0.1069	0.0537	-0.165	0.0034	0.3827	0.0161	-0.0103	0.7042	0.123	0.225	5.3266	-15.2974	69.4679
2	3.1365	1.9775	0.2043	2.6133	-2.1629	4.4666	0.2051	-1.2195	1.1786	0.8395	-0.0157	0.0001	-1.1221	-0.3212	-0.0407	0.5296	0.0595	-0.0484	0.773	-0.2028	0.3965	7.9464	-4.8278	70.1939
3	2.9367	0.4449	1.2192	4.8993	-0.4254	5.9798	-0.3634	-0.6982	2.2785	0.4296	0.0041	-0.309	-0.799	-0.0918	0.3495	0.3843	-0.0292	-0.1393	0.4994	-0.2108	0.7112	5.7338	0.209	64.5784
4	5.2935	-0.16	1.3559	3.6651	0.8304	1.7995	0.1091	-0.2255	0.0158	0.1088	-0.2061	-0.1072	0.0253	-0.0589	0.0659	0.1373	-0.0078	0.0101	0.1637	0.0072	0.1396	-3.7018	-13.1381	51.3078
5	8.1471	1.5471	3.1472	4.647	-3.8453	7.4749	0.2	-0.1076	-2.7384	-0.5389	0.3002	-0.7403	1.9377	0.3832	-0.6888	0.395	0.1099	-0.1658	0.3507	0.1193	0.6903	9.8628	-25.7639	58.0556
6	4.4806	0.1659	-0.0094	3.8474	0.679	5.5366	-0.0261	1.2414	0.4594	-0.9542	0.16	-0.1254	-0.3332	0.1259	-0.0332	0.3772	-0.0297	0.0021	0.4776	0.0407	0.2426	-12.4182	-14.006	8.6471
7	4.6733	0.8051	1.2695	1.8429	-0.1292	2.7744	-0.0816	0.403	0.518	-0.1968	-0.0277	0.1054	-0.1591	0.0525	0.0547	0.1813	0.0136	0.035	0.144	0.0184	0.1911	-6.9654	-12.0294	22.1371
8	5.9987	0.7583	-0.1926	4.3444	-0.0242	4.8486	0.1821	-0.873	0.2067	0.8828	0.0577	0.1256	-0.2561	0.0371	-0.1497	0.2723	0.0198	0.0025	0.2965	-0.0392	0.1826	-35.1036	3.4211	61.0698
9	4.8301	2.6162	-0.7828	3.1138	1.3803	3.7517	0.3225	-0.8754	-0.8645	0.5661	-0.2361	-0.1648	0.5299	0.0955	-0.2148	0.2786	-0.0278	-0.0543	0.5499	0.185	0.3325	-39.7502	-7.6107	61.6302
10	1.7857	-0.7941	-2.783	5.6061	1.8613	4.4586	-0.2484	-0.7358	-1.5572	0.6657	0.1975	-0.4782	0.9355	0.2444	-0.1191	0.392	-0.0083	-0.0704	0.4448	0.2075	0.6004	-31.3313	-12.9491	57.49
11	4.187	-0.5951	-0.684	3.1657	-0.8641	1.4376	0.0045	-0.0332	-0.1954	0.0363	-0.0037	-0.0709	0.0342	-0.0418	0.0042	0.166	-0.0013	-0.0165	0.1137	-0.0186	0.1112	-20.5695	-0.4072	47.5244
12	5.5785	1.1025	3.4263	7.7346	1.0894	7.344	0.3441	0.9642	1.3032	-0.5582	0.0113	0.2462	-0.8032	0.1406	-0.4062	0.3292	0.1295	0.099	0.3704	0.1339	0.4457	-36.0084	12.6731	47.726
13	5.8849	-1.2604	-0.5502	4.7349	0.6152	3.8369	0.3163	0.9273	0.358	-0.9143	-0.0678	-0.0838	-0.0677	-0.0062	-0.1336	0.2804	0.0004	-0.0199	0.3156	0.0624	0.1961	29.1761	0.6213	16.0103
14	8.9154	-2.4838	2.8405	2.4902	-1.5362	5.6404	1.067	0.7676	-0.9253	-0.3788	-0.1793	-0.0806	0.635	0.5817	-0.6561	0.2883	0.102	-0.0121	0.4713	-0.119	0.324	35.0364	-6.436	14.2758
15	3.9709	-1.0663	-2.0234	3.9049	-1.0553	4.4337	-0.0142	0.7899	-1.4585	-0.8755	0.3126	-0.1299	1.4786	0.5038	-0.1449	0.6185	-0.0043	-0.0691	0.3633	-0.2628	0.4106	28.318	-10.6055	18.0028
16	3.395	-1.8853	-2.6589	3.3471	-0.1088	3.2395	0.0386	0.1075	-1.1748	-0.2847	0.0025	-0.1602	0.401	0.5978	0.0187	0.267	0.0838	-0.0087	0.4007	-0.0733	0.3769	36.5021	-12.444	21.696
17	4.8543	0.0885	-4.273	2.2051	-0.7333	4.0727	-0.4651	1.1406	-1.7009	-1.4027	0.1444	-0.3858	0.7902	-0.8613	0.3836	0.8133	-0.0546	0.1402	0.5811	-0.1227	1.0995	20.2593	-18.6448	18.7348
18	4.455	-1.5353	-1.2801	5.9281	1.1593	1.8425	-0.034	0.4457	-0.0467	-0.1159	-0.206	-0.1239	0.082	0.0048	0.2393	0.1612	-0.0026	-0.0473	0.1983	0.007	0.1875	14.91	-5.5032	25.6838
19	4.5277	1.3985	1.2512	5.0993	0.5661	2.754	0.1728	-0.6163	0.1472	0.0147	-0.1847	0.04	0.0119	-0.0686	0.0122	0.1406	0	0.0269	0.1453	-0.0543	0.1806	12.446	0.734	33.7326
20	6.5636	-0.2273	-3.0793	2.1563	1.3082	4.239	-0.0251	-0.3257	1.0643	-0.3217	0.1047	-0.3807	-0.0961	0.3434	-0.134	0.2256	-0.0259	0.0303	0.1608	-0.0169	0.3536	24.9533	6.8813	26.8691
21	6.2826	-1.0249	-2.7898	2.8776	-0.0899	4.6309	-0.3354	-0.9514	1.4629	0.8928	-0.9015	0.3903	-0.5275	-0.1209	-0.1	0.2816	-0.3416	0.1235	0.4585	-0.4682	1.0329	28.3895	11.8209	33.2172

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 21 through 67 )	A	21 - 67
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 68 through 108 )	A	68 - 108
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 109 through 151 )	A	109 - 151
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 152 through 239 )	A	152 - 239
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 240 through 257 )	A	240 - 257
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 21 through 107 )	B	21 - 107
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 108 through 257 )	B	108 - 257
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 21 through 67 )	C	21 - 67
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 68 through 117 )	C	68 - 117
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 118 through 151 )	C	118 - 151
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 152 through 239 )	C	152 - 239
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 240 through 257 )	C	240 - 257
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 21 through 67 )	D	21 - 67
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 68 through 86 )	D	68 - 86
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 87 through 105 )	D	87 - 105
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 106 through 129 )	D	106 - 129
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 130 through 151 )	D	130 - 151
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 152 through 191 )	D	152 - 191
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 192 through 229 )	D	192 - 229
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 230 through 245 )	D	230 - 245
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 246 through 257 )	D	246 - 257

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