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: To Be Published
Title: Structure of Enterococcus faecium CdaA
Authors: Garbers, T.B. / Neumann, P. / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ofo.cif.gz	72 KB	Display	PDBx/mmCIF format
PDB format	pdb8ofo.ent.gz		Display	PDB format
PDBx/mmJSON format	8ofo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/of/8ofo ftp://data.pdbj.org/pub/pdb/validation_reports/of/8ofo	HTTPS FTP

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Related structure data

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 / Diethylene glycol diethyl ether Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈O₃
Has ligand of interest	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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