PDB-4xj4: Crystal structure of Vibrio cholerae DncV 3'-deoxy ATP bound form

ID or keywords:

Entry

Database: PDB / ID: 4xj4

Title

Crystal structure of Vibrio cholerae DncV 3'-deoxy ATP bound form

Components

Cyclic AMP-GMP synthase

Keywords

TRANSFERASE / Cyclic GMP-AMP synthase / Bacterial virulence / nucleotidyltransferase

Function / homology

Function and homology information

3',3'-cyclic GMP-AMP synthase activity / cyclic nucleotide biosynthetic process / negative regulation of chemotaxis / diguanylate cyclase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / GTP binding / ATP binding / metal ion binding
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.596 Å

Authors

Kato, K. / Ishii, R. / Ishitani, R. / Nureki, O.

Citation

Journal: Structure / Year: 2015
Title: Structural Basis for the Catalytic Mechanism of DncV, Bacterial Homolog of Cyclic GMP-AMP Synthase
Authors: Kato, K. / Ishii, R. / Hirano, S. / Ishitani, R. / Nureki, O.

History

Deposition	Jan 8, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 20, 2015	Group: Database references
Revision 1.2	Feb 5, 2020	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xj4.cif.gz	174.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4xj4_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4xj4_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4xj4_validation.xml.gz	18.5 KB	Display
Data in CIF	4xj4_validation.cif.gz	27.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xj/4xj4 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/4xj4	HTTPS FTP

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Related structure data

Related structure data	4xj1SC 4xj3C 4xj5C 4xj6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4xj3-d 6te6-1 5t2n-d 5go3-1 4lun-d 2p0o-d 6jzk-1 1q67-d 3liu-1 2atx-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
Related items in Molecule of the Month	#106 - Oct 2008 Poly(A) Polymerase similarity (1) #28 - Apr 2002 Anthrax Toxin similarity (1)

Deposited unit

A: Cyclic AMP-GMP synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	118.090, 51.300, 71.540
Angle α, β, γ (deg.)	90.00, 93.85, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-1126- HOH
2	1	A-1178- HOH

#1: Protein	Cyclic AMP-GMP synthase / c-AMP-GMP synthase / Dinucleotide cyclase DncV Mass: 44313.566 Da / Num. of mol.: 1 / Fragment: UNP residues 1-215,242-412 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: N16961 / Gene: dncV, VC_0179 / Production host: Escherichia coli (E. coli) References: UniProt: Q9KVG7, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₂P₃
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.58 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / pH: 8 / Details: PEG 3350, sodium malonate, Tris-HCl

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.596→50 Å / Num. obs: 55529 / % possible obs: 97.5 % / Redundancy: 3.4 % / Net I/σ(I): 18.8

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.9_1692)	refinement
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XJ1

4xj1

Resolution: 1.596→47.035 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.97 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2003	2773	4.99 %
R_work	0.1715	-	-
obs	0.173	55525	97.48 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.596→47.035 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2934	0	81	280	3295

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3133
X-RAY DIFFRACTION	f_angle_d	1.355	4246
X-RAY DIFFRACTION	f_dihedral_angle_d	15.605	1188
X-RAY DIFFRACTION	f_chiral_restr	0.057	462
X-RAY DIFFRACTION	f_plane_restr	0.006	541

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 (%)
1.5962-1.6237	0.2594	122	0.2501	2226	X-RAY DIFFRACTION	84
1.6237-1.6532	0.2665	136	0.2251	2640	X-RAY DIFFRACTION	96
1.6532-1.685	0.241	140	0.2035	2496	X-RAY DIFFRACTION	94
1.685-1.7194	0.2553	131	0.1933	2647	X-RAY DIFFRACTION	100
1.7194-1.7568	0.2299	133	0.194	2718	X-RAY DIFFRACTION	99
1.7568-1.7977	0.2284	156	0.1855	2669	X-RAY DIFFRACTION	100
1.7977-1.8427	0.1929	128	0.1743	2691	X-RAY DIFFRACTION	99
1.8427-1.8925	0.2237	144	0.1778	2662	X-RAY DIFFRACTION	99
1.8925-1.9482	0.1939	138	0.1794	2683	X-RAY DIFFRACTION	99
1.9482-2.011	0.2165	137	0.1831	2622	X-RAY DIFFRACTION	98
2.011-2.0829	0.2261	136	0.1881	2606	X-RAY DIFFRACTION	96
2.0829-2.1663	0.2239	137	0.1794	2602	X-RAY DIFFRACTION	97
2.1663-2.2649	0.1978	149	0.1677	2663	X-RAY DIFFRACTION	99
2.2649-2.3843	0.2057	137	0.171	2706	X-RAY DIFFRACTION	99
2.3843-2.5337	0.2086	146	0.177	2663	X-RAY DIFFRACTION	99
2.5337-2.7293	0.2007	137	0.1786	2686	X-RAY DIFFRACTION	99
2.7293-3.0039	0.2103	144	0.181	2602	X-RAY DIFFRACTION	95
3.0039-3.4385	0.1815	136	0.1777	2688	X-RAY DIFFRACTION	99
3.4385-4.3316	0.1928	144	0.1502	2707	X-RAY DIFFRACTION	99
4.3316-47.0555	0.1713	142	0.1518	2775	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	3.7242	-1.1573	-2.1172	4.465	2.9294	2.887	0.1556	0.0899	0.0053	-0.2121	-0.1752	0.1603	-0.0231	-0.0772	0.0536	0.1003	0.0055	-0.0064	0.113	0.0134	0.1428	5.6065	-11.1688	-5.232
2	2.2141	-1.9193	-2.9787	3.2697	4.3087	6.4957	0.1516	0.1089	-0.082	-0.3784	-0.1777	-0.0235	-0.7802	-0.2535	-0.0066	0.2961	0.0308	-0.0316	0.3321	-0.0529	0.18	19.5858	-32.8991	-45.6893
3	4.3184	-3.0322	-3.2562	2.1701	2.2754	2.4446	-0.3698	0.3341	-0.6717	0.6244	-0.3034	0.5426	0.8958	-0.4704	0.7081	0.3904	-0.0187	0.0483	0.2889	-0.0934	0.2856	14.5418	-39.973	-35.5735
4	1.385	0.8703	-0.2877	2.0774	1.4053	3.3424	0.0389	0.2821	-0.2939	-0.0313	-0.0057	-0.2192	0.238	-0.0047	0.0043	0.2441	0.0552	-0.0307	0.2676	-0.051	0.2152	17.4843	-30.6251	-26.5476
5	1.9405	-1.8748	-0.7876	7.0102	0.9219	4.6418	0.048	0.062	0.0999	-0.2158	0.0841	-0.2359	-0.4267	0.1061	-0.112	0.1952	0.009	-0.0025	0.2937	-0.0914	0.1802	20.3369	-28.4212	-33.4169
6	4.8171	-1.7065	-5.2108	3.1586	2.7398	8.7165	-0.1502	0.198	-0.3613	-0.03	-0.1351	0.1367	0.5474	0.2104	0.306	0.223	0.0324	-0.0495	0.2149	-0.01	0.2716	16.2595	-36.8102	-18.3968
7	3.6553	-0.6514	-0.4563	1.7522	0.1104	1.755	0.0131	-0.1201	-0.2878	-0.0048	-0.0215	0.1513	0.0732	0.0268	0.0064	0.1164	-0.0044	-0.0207	0.1014	0.014	0.1467	14.9758	-22.915	-4.077
8	5.8643	4.1268	3.5055	5.9364	1.9024	4.7908	0.2678	0.3521	-0.6693	0.0118	-0.0266	-0.2695	0.6348	0.2024	-0.2053	0.2149	0.0519	-0.0188	0.1533	-0.0183	0.2749	26.9481	-34.6743	-8.0342
9	1.9178	0.6538	1.022	7.2109	4.3228	3.3879	0.0142	-0.1867	-0.0857	0.1357	-0.0337	-0.2467	0.0378	0.2117	-0.1775	0.1126	-0.0076	-0.0238	0.1119	0.1138	0.076	24.7475	-16.4942	-0.3579
10	5.549	-1.1007	-1.8171	2.9298	2.9236	6.8649	0.1129	-0.1939	0.274	-0.077	-0.0063	-0.0207	-0.4147	-0.0042	-0.1124	0.1479	-0.0067	0.0044	0.0784	0.0131	0.1406	11.0959	-4.9792	-0.0823

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 25 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 26 through 93 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 94 through 117 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 118 through 150 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 151 through 245 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 246 through 277 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 278 through 338 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 339 through 360 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 361 through 382 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 383 through 412 )

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