PDB-6e0k: Structure of Rhodothermus marinus CdnE c-UMP-AMP synthase

ID or keywords:

Entry

Database: PDB / ID: 6e0k

Title

Structure of Rhodothermus marinus CdnE c-UMP-AMP synthase

Components

cGAS/DncV-like nucleotidyltransferase in E. coli homolog

Keywords

TRANSFERASE / cGAS / DncV / cyclic dinucleotide / nucleotide second messenger / nucleotidyltransferase

Function / homology

Function and homology information

nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / metal ion binding
Similarity search - Function

Biological species

Rhodothermus marinus SG0.5JP17-172 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.6 Å

Authors

Eaglesham, J.B. / Whiteley, A.T. / de Oliveira Mann, C.C. / Morehouse, B.R. / Nieminen, E.A. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.

Funding support

United States, 1items

Citation

Journal: Nature / Year: 2019
Title: Bacterial cGAS-like enzymes synthesize diverse nucleotide signals.
Authors: Whiteley, A.T. / Eaglesham, J.B. / de Oliveira Mann, C.C. / Morehouse, B.R. / Lowey, B. / Nieminen, E.A. / Danilchanka, O. / King, D.S. / Lee, A.S.Y. / Mekalanos, J.J. / Kranzusch, P.J.

History

Deposition	Jul 6, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 20, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2019	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 27, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6e0k.cif.gz	144.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6e0k_validation.pdf.gz	417.6 KB	Display	wwPDB validaton report
Full document	6e0k_full_validation.pdf.gz	418.9 KB	Display
Data in XML	6e0k_validation.xml.gz	16.7 KB	Display
Data in CIF	6e0k_validation.cif.gz	26.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e0/6e0k ftp://data.pdbj.org/pub/pdb/validation_reports/e0/6e0k	HTTPS FTP

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Related structure data

Related structure data	6e0lC 6e0mC 6e0nC 6e0oC 6m7kC C: citing same article (ref.)
Similar structure data	3qdq-d 5a9p-d 4otv-d 5gqm-d 5mqw-d 2oh7-d 5gqi-d 2oh6-d 5axv-d 2jj7-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

Deposited unit

A: cGAS/DncV-like nucleotidyltransferase in E. coli homolog

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	52.530, 66.330, 89.213
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	cGAS/DncV-like nucleotidyltransferase in E. coli homolog Mass: 34892.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodothermus marinus SG0.5JP17-172 (bacteria) Gene: Rhom172_2837 / Production host: Escherichia coli (E. coli) / References: UniProt: G2SLH8
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.23 Å³/Da / Density % sol: 44.77 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 10-20% ethanol, 100 mM Tris-HCl pH 7.5

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.00001 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.00001 Å / Relative weight: 1
Reflection	Resolution: 1.6→37.39 Å / Num. obs: 41925 / % possible obs: 99.7 % / Redundancy: 6.7 % / R_pim(I) all: 0.024 / Net I/σ(I): 18
Reflection shell	Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1925 / R_pim(I) all: 0.121 / % possible all: 95

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.6→37.389 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.37

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1863	2000	4.78 %	5
R_work	0.1635	-	-	-
obs	0.1646	41847	99.73 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.6→37.389 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2457	0	0	442	2899

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2530
X-RAY DIFFRACTION	f_angle_d	0.802	3427
X-RAY DIFFRACTION	f_dihedral_angle_d	12.491	1491
X-RAY DIFFRACTION	f_chiral_restr	0.051	341
X-RAY DIFFRACTION	f_plane_restr	0.006	446

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 (%)
1.5987-1.6387	0.2286	137	0.1851	2727	X-RAY DIFFRACTION	97
1.6387-1.683	0.2328	140	0.1707	2804	X-RAY DIFFRACTION	100
1.683-1.7325	0.2052	141	0.1686	2796	X-RAY DIFFRACTION	100
1.7325-1.7884	0.2097	141	0.1711	2824	X-RAY DIFFRACTION	100
1.7884-1.8524	0.1926	142	0.1598	2817	X-RAY DIFFRACTION	100
1.8524-1.9265	0.194	142	0.1705	2823	X-RAY DIFFRACTION	100
1.9265-2.0142	0.1824	142	0.1741	2849	X-RAY DIFFRACTION	100
2.0142-2.1204	0.198	143	0.162	2833	X-RAY DIFFRACTION	100
2.1204-2.2532	0.1821	141	0.1611	2813	X-RAY DIFFRACTION	100
2.2532-2.4272	0.1855	143	0.1665	2849	X-RAY DIFFRACTION	100
2.4272-2.6713	0.1909	144	0.1702	2871	X-RAY DIFFRACTION	100
2.6713-3.0577	0.1805	145	0.168	2873	X-RAY DIFFRACTION	100
3.0577-3.8518	0.1677	146	0.1573	2920	X-RAY DIFFRACTION	100
3.8518-37.3994	0.183	153	0.1552	3048	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	0.888	0.177	-0.4042	0.4205	0.1216	0.2333	0.0506	0.1088	-0.0842	0.0121	0.045	-0.0723	0.0264	0.1483	0.0057	0.1256	-0.003	-0.0122	0.1326	0.0101	0.1101	29.8388	32.1476	51.2692
2	0.2983	0.1255	-0.2525	0.0531	-0.1638	0.3005	0.0023	0.0318	0.0314	0.0054	0.0476	0.0511	-0.0947	0.0686	0.0001	0.1412	-0.006	-0.0096	0.1315	0.0075	0.1248	28.8682	33.5997	59.134
3	1.8421	0.0141	-0.7948	1.2905	-0.65	1.8251	-0.0374	-0.1792	-0.01	0.2084	0.0387	-0.0606	-0.2042	0.1294	0.024	0.1334	-0.0019	-0.0219	0.1089	-0.006	0.1164	35.5193	30.3211	84.3982
4	0.5914	-0.2732	-0.4086	0.1287	0.1044	0.9971	0.1638	-0.0795	0.1675	0.1458	0.0189	-0.0812	-0.6556	0.076	0.1196	0.2101	-0.0371	-0.0008	0.1458	-0.018	0.1505	39.0984	45.0742	63.6545
5	0.7855	-0.1796	-0.3152	0.1546	0.1698	1.1992	0.0285	-0.0513	0.029	0.0834	0.1356	0.0381	-0.0537	-0.1899	0.0546	0.1306	-0.0121	0.0056	0.1251	-0.0185	0.1105	30.3577	35.6556	66.8406
6	0.4653	0.2692	0.3439	0.2606	0.0879	0.2603	0.0532	-0.0456	-0.0399	0.0437	-0.0604	0.0489	0.0433	-0.0236	-0.0066	0.1297	-0.0026	0.0038	0.1453	0.0236	0.1329	22.3916	26.5824	61.8704
7	1.0592	0.0304	-0.1817	0.4649	0.2701	0.6624	0.0254	0.1766	0.2186	-0.0076	-0.0746	-0.0381	-0.0589	0.0511	-0.0245	0.1072	-0.0098	-0.0166	0.0995	0.0067	0.1134	11.7454	29.5657	47.0616
8	1.2306	-0.055	-0.1453	0.5671	-0.3821	0.8148	-0.0271	-0.0099	-0.0883	0.0085	0.0398	0.1584	-0.0237	0.0013	0.0142	0.1141	0.0007	-0.0112	0.1089	0.0042	0.1428	7.8373	24.2272	53.0174
9	2.0897	0.4806	0.1727	2.4931	-1.3612	1.3005	-0.0481	-0.9416	0.3211	0.6711	0.0687	0.1272	-0.4442	-0.1	0.1451	0.2578	0.0133	0.0138	0.2878	-0.0473	0.1647	10.7855	28.6711	66.9685
10	0.7118	-0.6657	0.2016	0.5458	-0.254	0.9248	0.0327	-0.0389	-0.1212	-0.0222	0.0905	0.1393	-0.0502	-0.2521	0.1406	0.1273	0.0175	0.0077	0.1653	0.0185	0.1914	-5.1018	31.9465	46.3673

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 50 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 51 through 73 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 74 through 91 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 92 through 107 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 108 through 157 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 158 through 185 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 186 through 202 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 203 through 244 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 245 through 268 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 269 through 296 )

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