PDB-4txy: Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase...

ID or keywords:

Entry

Database: PDB / ID: 4txy

Title

Crystal structure of Vibrio cholerae DncV cyclic AMP-GMP synthase, a prokaryotic cGAS homolog

Components

Cyclic AMP-GMP synthase

Keywords

TRANSFERASE / nucleotidyl transferase / cyclic nucleotide synthase / cGAS

Function / homology

Function and homology information

3',3'-cyclic GMP-AMP synthase activity / cyclic nucleotide biosynthetic process / diguanylate cyclase activity / negative regulation of chemotaxis / 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 /

SAD / Resolution: 3.0001 Å

Authors

Kranzusch, P.J. / Lee, A.S.Y. / Wilson, S.C. / Solovykh, M.S. / Vance, R.E. / Berger, J.M. / Doudna, J.A.

Funding support

United States, 2items

Citation

Journal: Cell / Year: 2014
Title: Structure-Guided Reprogramming of Human cGAS Dinucleotide Linkage Specificity.
Authors: Kranzusch, P.J. / Lee, A.S. / Wilson, S.C. / Solovykh, M.S. / Vance, R.E. / Berger, J.M. / Doudna, J.A.

History

Deposition	Jul 7, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 13, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 3, 2014	Group: Database references
Revision 1.2	Oct 1, 2014	Group: Database references
Revision 1.3	Feb 4, 2015	Group: Derived calculations
Revision 1.4	Nov 20, 2019	Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy / Structure summary Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_keywords Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.5	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4txy.cif.gz	306.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4txy.ent.gz	252.7 KB	Display	PDB format
PDBx/mmJSON format	4txy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tx/4txy ftp://data.pdbj.org/pub/pdb/validation_reports/tx/4txy	HTTPS FTP

-
Related structure data

Related structure data	4txzC 4ty0C C: citing same article (ref.)
Similar structure data	4u0l-2 4ygf-3 5tv3-4 5tuo-4 4xfw-d 5tuo-3 4u0n-1 5tuo-2 5tt8-4 4ygf-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Cyclic AMP-GMP synthase

B: Cyclic AMP-GMP synthase

hetero molecules

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

1

A: Cyclic AMP-GMP synthase

hetero molecules

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

2

B: Cyclic AMP-GMP synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	70.167, 59.116, 102.539
Angle α, β, γ (deg.)	90.00, 95.48, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cyclic AMP-GMP synthase / c-AMP-GMP synthase / Dinucleotide cyclase DncV Mass: 46966.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: dncV, VC_0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KVG7, cyclic GMP-AMP synthase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

#1: Protein

Cyclic AMP-GMP synthase / c-AMP-GMP synthase / Dinucleotide cyclase DncV

Mass: 46966.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: dncV, VC_0179 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9KVG7, cyclic GMP-AMP synthase

#2: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.25 Å³/Da / Density % sol: 45.42 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 30 mM HEPES-KOH pH 7.5, 200-300 mM Mg(OAc)2 and 20-22% PEG-3350

-
Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 3→45.12 Å / Num. obs: 16701 / % possible obs: 98 % / Redundancy: 3.5 % / Net I/σ(I): 6.4
Reflection shell	Resolution: 3→3.16 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.3 / % possible all: 98.6

-
Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement

Refinement

Method to determine structure:

SAD / Resolution: 3.0001→45.12 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2504	427	2.56 %	10
R_work	0.2253	-	-	-
obs	0.2259	16670	97.68 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.0001→45.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5910	0	2	0	5912

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6024
X-RAY DIFFRACTION	f_angle_d	0.805	8118
X-RAY DIFFRACTION	f_dihedral_angle_d	16.679	2300
X-RAY DIFFRACTION	f_chiral_restr	0.03	890
X-RAY DIFFRACTION	f_plane_restr	0.004	1048

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 (%)
3.0001-3.4341	0.3442	142	0.3048	5424	X-RAY DIFFRACTION	99
3.4341-4.326	0.218	138	0.2275	5289	X-RAY DIFFRACTION	96
4.326-45.1287	0.2339	147	0.1923	5530	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	2.9304	0.3339	0.6393	3.7355	-0.5554	4.3292	0.0446	0.0105	0.103	0.0117	0.3068	0.382	-0.2708	0.7617	-0.2469	0.3828	0.0617	0.0412	0.3898	-0.0313	0.465	-37.0803	50.1952	117.4891
2	2.394	1.1505	2.0937	3.5557	1.5417	5.2198	0.1857	0.9444	-0.0229	-0.4334	0.325	-0.0242	-0.1163	0.3421	-0.4387	0.4017	-0.0583	0.0536	0.538	0.0821	0.4416	-58.9286	39.0686	87.8385
3	5.1278	-1.5992	1.0656	3.9216	0.9349	3.2973	-0.1525	0.686	-0.2335	-0.265	0.3393	1.5382	0.6919	-0.4648	-0.276	0.6588	-0.2066	0.0508	0.7965	0.0405	1.0644	-75.1315	27.726	84.2809
4	4.1921	-2.0284	2.3321	4.0607	-0.4939	3.534	-1.1582	0.155	0.9684	0.1842	0.6266	0.2622	-0.9703	-0.1056	0.0532	0.7178	0.0736	-0.0036	0.9168	0.1651	0.9184	-67.5363	46.0276	89.413
5	2.2021	-0.3732	3.7745	1.6292	-0.6596	5.1735	-0.0222	-0.1035	-0.4478	-0.0743	0.2049	0.3372	0.1679	-0.2617	-0.0586	0.7491	-0.014	-0.0144	0.4411	0.0681	0.5722	-57.9129	43.191	103.1123
6	2.0796	-0.4814	0.1331	4.302	-1.1044	2.2136	0.1109	-0.2702	-0.3305	0.4539	0.1405	0.533	0.1003	-0.3139	-0.08	0.5545	-0.0161	0.0565	0.4943	0.062	0.4292	-62.2392	32.507	98.2983
7	0.5421	0.0098	0.0843	3.0347	-0.1267	4.201	-0.2068	0.1456	0.5473	0.1745	0.256	0.3698	-1.1089	-0.3343	-0.1707	0.5981	0.0255	0.0325	0.5833	0.033	0.7366	-66.4947	51.5826	94.6068
8	2.8062	-0.2577	3.3178	2.8676	1.3148	3.8221	-0.7837	0.8803	0.6396	0.2044	0.6334	0.9105	-0.3754	0.074	0.2535	0.7308	0.2282	0.115	0.5642	0.0334	0.6075	-64.2231	53.4401	105.3976
9	3.3313	0.0721	-0.5469	5.0826	0.583	1.9137	0.0135	-0.4168	0.2472	0.2783	0.061	0.0786	-0.2789	-0.2919	-0.0445	0.4009	0.1494	-0.025	0.4437	-0.0116	0.3241	-51.7242	53.9095	120.579
10	3.5114	-0.3379	-0.6381	3.4351	-2.0283	8.2141	-0.1671	-0.2601	-0.0375	-0.7247	0.0544	0.095	-0.1711	-0.9168	-0.8435	0.674	0.0938	-0.1499	0.6528	0.0584	0.7646	-68.8438	53.2235	119.5094
11	5.3759	-0.1995	-0.383	2.7303	-1.9154	3.3728	0.7084	-1.4883	-0.1558	0.3347	-0.215	0.1935	0.2446	-0.5012	-0.1587	0.5389	0.2479	-0.0178	0.8013	0.0232	0.5062	-54.0153	47.2696	130.3094
12	3.3725	0.4337	-0.6952	4.3705	0.1792	2.452	0.1982	-1.1292	-0.1186	0.6669	-0.085	-0.4312	0.1955	0.427	0.0447	0.6157	0.1414	-0.0148	0.7952	0.0295	0.4537	-35.3663	47.6106	127.396
13	2.5568	0.9384	-0.267	3.9605	-1.8255	2.5903	0.2908	-0.305	-0.5756	0.1081	-0.2242	-0.5882	-0.5796	0.2781	-0.059	0.4566	-0.0304	0.018	0.5168	0.054	0.5475	-30.5049	51.0632	65.4834
14	1.2975	0.615	0.6469	4.9103	1.5474	3.9442	0.4287	0.8656	0.0526	-0.3607	-0.0385	-0.2345	-0.041	0.1828	-0.3636	0.4236	0.0945	0.0265	0.533	-0.001	0.3138	-55.2996	40.1713	38.235
15	2.9998	-2.0543	2.9053	2.4529	-0.4443	5.1119	0.1272	-0.0298	-0.7131	-0.0447	0.3121	0.9514	0.4462	-1.1457	-0.4227	0.7867	-0.1116	-0.0419	0.9009	-0.1125	0.9111	-72.0775	29.1054	36.6247
16	2.4155	0.5731	-0.691	4.0616	0.7631	4.8299	-0.4494	0.1438	1.4427	-0.4781	0.111	0.4132	-0.8595	-0.4256	0.5824	0.8504	0.0905	-0.0223	0.7133	-0.0398	0.8586	-63.7707	47.3138	40.7555
17	2.612	0.7358	1.4862	1.6994	1.4821	2.4485	-0.2223	0.2236	0.2436	0.1426	-0.1049	-0.1348	-0.2627	-0.1329	-0.0364	0.6715	-0.0476	-0.0274	0.5323	0.0236	0.4939	-52.0114	44.1932	53.863
18	2.9168	0.8334	0.6469	6.5761	1.8674	5.9104	0.3148	-0.4121	-0.0089	0.344	-0.0874	0.2572	-0.0588	-0.7823	-0.0875	0.3972	-0.0021	0.087	0.5141	-0.0608	0.4038	-57.6986	33.6051	49.0991
19	3.8075	2.0564	1.656	4.3382	2.5136	6.3149	0.286	0.8993	1.2148	-0.7634	-0.6474	0.5744	-0.5721	-0.8607	0.1069	0.5805	0.1274	0.0283	0.6529	0.1068	0.6566	-62.33	50.0186	48.259
20	2.5162	-0.2058	2.6613	3.0124	0.9719	4.4198	-0.5133	-0.1373	0.7768	-0.157	-0.0652	0.8328	-0.3635	-0.6398	0.359	0.518	0.1801	0.0988	0.5365	-0.0575	0.5433	-58.5301	54.7215	56.2559
21	4.1767	0.8855	1.345	3.1518	0.4608	3.4593	0.4357	-0.5105	0.1302	0.4821	-0.4192	0.3377	-0.0438	-0.2227	0.0535	0.4489	-0.133	0.0181	0.4396	-0.1002	0.3964	-44.6286	55.0904	70.0471
22	2.5719	-0.2915	0.2457	8.0402	-5.5952	4.3768	0.4205	0.1024	0.5839	0.251	0.3836	0.6416	-0.6242	-1.7258	-2.0804	0.5863	-0.1407	0.1318	0.8671	-0.1464	0.887	-61.6413	54.6827	70.781
23	5.9029	1.1313	0.4025	2.471	0.7201	1.8727	0.3601	-1.3344	-0.1419	0.3476	-0.364	-0.1375	0.0873	-0.4802	0.1043	0.7829	-0.2142	0.0156	0.8984	0.0925	0.4239	-45.825	48.606	80.0704
24	3.7165	0.0537	-2.3397	2.5915	-0.0787	4.3629	0.1003	-1.3036	-0.473	0.7153	-0.1944	-0.9306	1.0419	0.7988	0.2101	0.7764	-0.0962	-0.204	0.7575	0.2618	0.735	-28.2205	47.2789	75.0252

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 5 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 60 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 61 through 94 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 118 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 119 through 151 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 152 through 189 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 190 through 249 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 250 through 278 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 279 through 339 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 340 through 361 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 362 through 382 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 383 through 413 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 5 through 26 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 27 through 60 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 61 through 94 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 95 through 118 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 119 through 151 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 152 through 189 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 190 through 249 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 250 through 278 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 279 through 339 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 340 through 361 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid 362 through 382 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 383 through 411 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi