PDB-8jsf: Crystal structure of a cytidylate cyclase from multidrug-resistan...

ID or keywords:

Entry

Database: PDB / ID: 8jsf

Title

Crystal structure of a cytidylate cyclase from multidrug-resistant bacterium Elizabethkingia anopheles

Components

cytidylate cyclase

Keywords

TRANSFERASE / Adenylate/guanylate cyclase

Biological species

Elizabethkingia anophelis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Wang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.

Funding support

Taiwan, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Structural and functional characterization of cyclic pyrimidine-regulated anti-phage system.
Authors: Hou, M.H. / Chen, C.J. / Yang, C.S. / Wang, Y.C. / Chen, Y.

History

Deposition	Jun 20, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 3, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jul 17, 2024	Group: Database references / Structure summary / Category: citation / citation_author / entity Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _entity.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8jsf.cif.gz	226.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8jsf.ent.gz	182.8 KB	Display	PDB format
PDBx/mmJSON format	8jsf.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8jsf_validation.pdf.gz	436.1 KB	Display	wwPDB validaton report
Full document	8jsf_full_validation.pdf.gz	440.2 KB	Display
Data in XML	8jsf_validation.xml.gz	22.9 KB	Display
Data in CIF	8jsf_validation.cif.gz	33.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/js/8jsf ftp://data.pdbj.org/pub/pdb/validation_reports/js/8jsf	HTTPS FTP

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Related structure data

Related structure data	8jsjC 8jskC 8jszC C: citing same article (ref.)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: cytidylate cyclase

B: cytidylate cyclase

78.9 kDa, 2 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)	164.483, 164.483, 164.483
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	197
Space group name H-M	I23

Components on special symmetry positions

ID	Model	Components
1	1	A-492- HOH
2	1	A-502- HOH
3	1	A-533- HOH

#1: Protein	cytidylate cyclase Mass: 39472.184 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: NCBI:WP_049037095.1 / Source: (gene. exp.) Elizabethkingia anophelis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: cytidylate cyclase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.35 Å³/Da / Density % sol: 47.63 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.05 M Bis-Tris 7.0, 1.6 M Ammonium sulfate, 25% v/v Glycerol, 0.15 M Potassium chloride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97624 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Oct 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97624 Å / Relative weight: 1
Reflection	Resolution: 2.2→30 Å / Num. obs: 37544 / % possible obs: 99.9 % / Redundancy: 33.9 % / CC_1/2: 0.998 / Net I/σ(I): 51
Reflection shell	Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3697 / CC_1/2: 0.835 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.2-4158)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.2→22.38 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.03 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2157	1884	5.02 %
R_work	0.179	-	-
obs	0.1809	37525	99.95 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→22.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4078	0	0	353	4431

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4182
X-RAY DIFFRACTION	f_angle_d	0.678	5642
X-RAY DIFFRACTION	f_dihedral_angle_d	13.453	1512
X-RAY DIFFRACTION	f_chiral_restr	0.05	584
X-RAY DIFFRACTION	f_plane_restr	0.004	723

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 (%)
2.2-2.26	0.2711	141	0.2434	2714	X-RAY DIFFRACTION	99
2.26-2.33	0.2874	148	0.2291	2707	X-RAY DIFFRACTION	100
2.33-2.4	0.2393	143	0.2284	2725	X-RAY DIFFRACTION	100
2.4-2.49	0.293	142	0.2193	2708	X-RAY DIFFRACTION	100
2.49-2.59	0.2846	146	0.2198	2748	X-RAY DIFFRACTION	100
2.59-2.7	0.2324	143	0.2146	2730	X-RAY DIFFRACTION	100
2.7-2.85	0.2678	140	0.2108	2722	X-RAY DIFFRACTION	100
2.85-3.02	0.2508	145	0.2027	2724	X-RAY DIFFRACTION	100
3.02-3.26	0.2295	143	0.1906	2741	X-RAY DIFFRACTION	100
3.26-3.58	0.2035	147	0.1622	2742	X-RAY DIFFRACTION	100
3.58-4.1	0.1781	143	0.1416	2750	X-RAY DIFFRACTION	100
4.1-5.15	0.1634	151	0.1333	2779	X-RAY DIFFRACTION	100
5.16-22.38	0.1876	152	0.1716	2851	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	0.1186	0.0005	-0.0979	0.3616	0.0733	0.3335	0.1167	-0.2665	-0.07	0.1369	-0.4881	0.1524	0.1992	-0.6384	-0.431	0.3287	-0.2481	-0.0764	0.3356	0.0232	0.4066	110.2148	64.3884	20.5188
2	0.3458	0.1213	0.3038	0.3358	0.0394	0.5485	0.4646	-0.7371	0.1066	0.2968	-0.5295	0.1496	0.4994	-0.8474	0.4034	0.1671	-0.1081	-0.0626	0.2096	-0.0153	0.3194	116.5406	68.5913	22.7763
3	0.0018	0.0206	-0.022	0.1928	-0.156	0.13	-0.0342	-0.0905	0.1427	0.0236	-0.2185	0.0302	0.0827	-0.052	-0.0709	0.1778	-0.0229	-0.0042	0.3485	-0.1252	0.2922	111.4451	76.5065	22.1209
4	0.6685	0.3126	0.3547	0.5266	0.1302	0.5745	0.2834	-0.6144	0.2698	-0.0111	-0.5391	0.3235	0.2688	-0.9494	-0.3693	0.193	-0.2644	-0.0046	0.515	-0.1853	0.272	115.5854	75.8085	30.0802
5	0.0451	-0.0343	0.0355	0.0558	0.0453	0.1258	-0.0661	-0.2332	0.1349	0.1153	-0.2843	0.1261	0.0005	-0.4332	-0.1966	0.2397	-0.3046	-0.067	0.5243	-0.6219	-0.0759	122.7948	85.7424	40.7048
6	0.0078	-0.0082	-0.0101	0.0133	-0.0174	0.1352	0.0318	-0.2562	0.1234	0.0298	0.0922	0.0406	0.0245	-0.3879	0.1737	0.3996	-0.3674	0.1304	0.7679	-0.4976	0.0986	111.8936	79.9976	40.7445
7	0.1734	-0.0441	0.0444	0.0706	0.0101	0.1812	-0.0703	0.1248	0.0049	-0.1803	-0.0848	-0.0694	-0.2067	-0.0032	-0.2009	0.2768	-0.0588	-0.0776	0.1708	0.038	0.1799	132.2465	82.9092	6.4517
8	0.3829	-0.0126	0.324	0.0383	-0.0097	0.1364	-0.1037	-0.0113	0.0877	-0.1697	0.0842	0.2264	-0.0767	0.0324	0.0384	0.2244	-0.0219	-0.0802	0.159	-0.01	0.2197	127.874	76.6023	13.7712
9	0.0405	-0.0256	0.0342	0.0602	-0.0237	0.0115	0.028	0.0383	-0.1984	0.0125	0.1237	0.1016	0.0625	0.0115	0.1175	0.1614	-0.032	-0.0575	0.1335	-0.0295	0.1514	130.0291	69.4357	9.8606
10	0.2362	-0.0857	0.2731	0.0597	-0.0369	0.159	-0.0415	0.0253	-0.0272	0.2128	0.1055	-0.1653	-0.0173	0.1851	0.065	0.2132	-0.0326	-0.0621	0.1789	-0.0318	0.1735	140.3558	78.4317	15.3734
11	0.033	0.0716	-0.0321	0.0537	-0.037	0.0936	0.4078	-0.0495	-0.2809	0.28	-0.0743	0.0615	0.0633	-0.0966	0.1429	0.1554	-0.0503	-0.2117	0.1414	0.048	0.1325	126.1075	62.0294	17.3587
12	0.2513	0.0413	-0.2767	0.0988	-0.0577	0.3249	0.3146	-0.0519	-0.2348	0.1058	0.0128	-0.0799	0.1115	0.152	0.2329	0.1899	0.0372	-0.2001	0.136	-0.0348	0.275	143.7886	66.3633	18.2177
13	0.1369	-0.0187	0.0452	0.0105	-0.0208	0.0813	0.4483	-0.1538	-0.3589	0.0187	0.134	-0.063	0.4382	-0.0145	0.4986	0.3765	-0.0798	-0.3864	0.1915	0.3176	0.1701	143.7408	61.6797	27.6108
14	0.1298	-0.1585	-0.1222	0.1887	0.1589	0.1811	0.4946	0.1532	-0.4042	-0.0142	0.2575	-0.2456	0.2134	0.1795	0.4338	0.2002	0.0088	-0.2627	0.2196	0.0202	0.2831	147.1314	66.4523	18.4789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 85 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 86 through 135 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 158 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 159 through 252 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 253 through 280 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 281 through 300 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 82 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 135 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 136 through 158 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 159 through 203 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 204 through 236 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 237 through 252 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 253 through 280 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 281 through 298 )

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