PDB-8ofo: Structure of Enterococcus faecium CdaA

ID or keywords:

Entry

Database: PDB / ID: 8ofo

Title

Structure of Enterococcus faecium CdaA

Components

Diadenylate cyclase

Keywords

TRANSFERASE / Diadenylate cyclase

Function / homology

Function and homology information

: / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / nucleotidyltransferase activity / ATP binding / plasma membrane
Similarity search - Function

Biological species

Enterococcus faecium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.45 Å

Authors

Garbers, T.B. / Neumann, P. / Ficner, R.

Funding support

Germany, 1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2024
Title: Crystallographic fragment screen of the c-di-AMP-synthesizing enzyme CdaA from Bacillus subtilis.
Authors: Garbers, T. / Neumann, P. / Wollenhaupt, J. / Dickmanns, A. / Weiss, M.S. / Ficner, R.

History

Deposition	Mar 16, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 21, 2023	Provider: repository / Type: Initial release
Revision 1.1	Jun 19, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2	May 14, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._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 / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

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Related structure data

Related structure data	8ofhC 8ogmC 8ognC 8ogoC 8ogpC 8ogqC 8ogrC 8ogsC 8ogtC 8oguC 8ogvC 8ogwC 8ogyC 8ogzC 8oh0C 8oh1C 8ohbC 8ohcC 8oheC 8ohfC 8ohgC 8ohhC 8ohjC 8ohkC 8ohlC 8ohoC 9g0gC C: citing same article (ref.)
Similar structure data	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

AAA: Diadenylate cyclase

BBB: Diadenylate cyclase

hetero molecules

33.2 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)	99.160, 99.160, 112.180
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	182
Space group name H-M	P6₃22

#1: Protein	Diadenylate cyclase Mass: 16538.930 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: dacA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A855P6J0
#2: Chemical	ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₃
Has ligand of interest	N
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 48.89 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1.5 M Lithium sulfate 0.05 M TRIS pH 8.5 5 % (v/v) Glycerol 0.005 M Magnesium chloride

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P14 (MX2) / Wavelength: 0.976264 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.976264 Å / Relative weight: 1

Reflection

Resolution: 2.45→50 Å / Num. obs: 12518 / % possible obs: 100 % / Redundancy: 37 % / CC_1/2: 0.998 / R_merge(I) obs: 0.379 / R_rim(I) all: 0.385 / Net I/σ(I): 17.4

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.45-2.51	3.429	884	0.792	3.473	1
2.51-2.58	2.987	889	0.855	3.027	1
2.58-2.66	2.577	851	0.92	2.611	1
2.66-2.74	2.152	840	0.966	2.18	1
2.74-2.83	1.779	802	0.978	1.803	1
2.83-2.93	1.718	785	0.985	1.741	1
2.93-3.04	1.291	754	0.994	1.309	1
3.04-3.16	1.029	732	0.994	1.043	1
3.16-3.3	0.933	705	0.997	0.945	1
3.3-3.46	0.746	672	0.997	0.756	1
3.46-3.65	0.518	658	0.997	0.525	1
3.65-3.87	0.355	603	0.998	0.36	1
3.87-4.14	0.296	590	0.998	0.3	1
4.14-4.47	0.193	533	0.998	0.196	1
4.47-4.9	0.15	505	0.998	0.152	1
4.9-5.48	0.172	468	0.999	0.175	1
5.48-6.33	0.147	411	0.998	0.149	1
6.33-7.75	0.11	358	0.999	0.112	1
7.75-10.96	0.081	295	0.999	0.083	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.45→49.58 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.903 / SU B: 9.028 / SU ML: 0.204 / Cross valid method: FREE R-VALUE / ESU R: 0.467 / ESU R Free: 0.3
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2743	626	5.002 %
R_work	0.2053	11890	-
all	0.209	-	-
obs	-	12516	99.952 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 55.996 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.246 Å²	-0.123 Å²	0 Å²
2-	-	-0.246 Å²	-0 Å²
3-	-	-	0.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.45→49.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2285	0	11	0	2296

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	2312
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	2296
X-RAY DIFFRACTION	r_angle_refined_deg	1.631	1.632	3127
X-RAY DIFFRACTION	r_angle_other_deg	1.254	1.572	5304
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.907	5	295
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.959	23.585	106
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.25	15	434
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.273	15	12
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	335
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	2551
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	449
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	432
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.186	0.2	2223
X-RAY DIFFRACTION	r_nbtor_refined	0.152	0.2	1133
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1258
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	49
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.312	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.205	0.2	51
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.141	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	4.987	5.556	1186
X-RAY DIFFRACTION	r_mcbond_other	4.987	5.554	1185
X-RAY DIFFRACTION	r_mcangle_it	6.637	8.342	1479
X-RAY DIFFRACTION	r_mcangle_other	6.634	8.344	1480
X-RAY DIFFRACTION	r_scbond_it	6.405	6.417	1126
X-RAY DIFFRACTION	r_scbond_other	6.402	6.42	1127
X-RAY DIFFRACTION	r_scangle_it	9.296	9.298	1647
X-RAY DIFFRACTION	r_scangle_other	9.293	9.3	1648
X-RAY DIFFRACTION	r_lrange_it	11.931	109.279	9404
X-RAY DIFFRACTION	r_lrange_other	11.93	109.28	9405

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
2.45-2.514	0.369	44	0.281	838	0.285	882	0.783	0.834	100	0.258
2.514-2.582	0.457	44	0.262	841	0.271	885	0.772	0.858	100	0.23
2.582-2.657	0.281	43	0.234	810	0.237	853	0.885	0.892	100	0.204
2.657-2.738	0.301	41	0.22	792	0.224	834	0.904	0.918	99.8801	0.19
2.738-2.828	0.229	41	0.199	765	0.201	806	0.927	0.939	100	0.177
2.828-2.927	0.366	39	0.201	741	0.208	780	0.867	0.934	100	0.177
2.927-3.037	0.281	37	0.184	713	0.188	750	0.921	0.945	100	0.164
3.037-3.16	0.231	37	0.183	696	0.185	733	0.922	0.944	100	0.167
3.16-3.3	0.235	35	0.19	669	0.192	704	0.94	0.942	100	0.171
3.3-3.461	0.214	34	0.213	638	0.213	672	0.942	0.933	100	0.203
3.461-3.647	0.291	32	0.199	615	0.204	648	0.918	0.94	99.8457	0.191
3.647-3.867	0.256	31	0.169	584	0.174	615	0.915	0.956	100	0.168
3.867-4.132	0.304	29	0.179	549	0.184	578	0.912	0.953	100	0.178
4.132-4.461	0.188	27	0.164	516	0.165	543	0.959	0.962	100	0.172
4.461-4.882	0.279	25	0.16	480	0.166	506	0.94	0.968	99.8024	0.171
4.882-5.452	0.333	23	0.192	436	0.199	459	0.934	0.96	100	0.192
5.452-6.283	0.304	21	0.248	400	0.25	421	0.901	0.93	100	0.254
6.283-7.664	0.302	18	0.244	345	0.247	363	0.901	0.907	100	0.248
7.664-10.711	0.195	15	0.235	276	0.233	291	0.951	0.932	100	0.252
10.711-49.58	0.308	10	0.327	187	0.326	197	0.917	0.911	100	0.374

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