PDB-8ofj: Mycoplasma pneumoniae CdaM

ID or keywords:

Entry

Database: PDB / ID: 8ofj

Title

Mycoplasma pneumoniae CdaM

Components

Diadenylate cyclase

Keywords

TRANSFERASE / diadenylate cyclase

Function / homology

Function and homology information

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

Biological species

Mycoplasmoides pneumoniae 19294 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

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

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Streptococcus pneumoniae CdaA
Authors: Garbers, T.B. / Neumann, P. / Ficner, R.

History

Deposition	Mar 15, 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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Validation report

Summary document	8ofj_validation.pdf.gz	432.4 KB	Display	wwPDB validaton report
Full document	8ofj_full_validation.pdf.gz	433.9 KB	Display
Data in XML	8ofj_validation.xml.gz	12.7 KB	Display
Data in CIF	8ofj_validation.cif.gz	16.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/of/8ofj ftp://data.pdbj.org/pub/pdb/validation_reports/of/8ofj	HTTPS FTP

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Related structure data

Related structure data	8ofhC 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

B: Diadenylate cyclase

A: Diadenylate cyclase

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

1

A: Diadenylate cyclase

B: Diadenylate cyclase

defined by author
Evidence: gel filtration
36.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	38.840, 80.420, 44.444
Angle α, β, γ (deg.)	90.000, 93.130, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Diadenylate cyclase / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylyl cyclase Mass: 18397.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycoplasmoides pneumoniae 19294 (bacteria) Gene: dacB, MPN_244, K04_orf202, MP588 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P75528, diadenylate cyclase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Diadenylate cyclase / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylyl cyclase

Mass: 18397.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycoplasmoides pneumoniae 19294 (bacteria)
Gene: dacB, MPN_244, K04_orf202, MP588 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P75528, diadenylate cyclase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 54 / 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: 1.88 Å³/Da / Density % sol: 34.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% (v/v) PEG MME 2000 0.1M Na-HEPES pH 7.5

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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: P13 (MX1) / Wavelength: 0.97626 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.97626 Å / Relative weight: 1

Reflection

Resolution: 2.25→50 Å / Num. obs: 12934 / % possible obs: 99.3 % / Redundancy: 6.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.122 / R_rim(I) all: 0.132 / Net I/σ(I): 11.68

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.25-2.31	1.308	958	0.639	1.412	1
2.31-2.37	1.133	907	0.722	1.223	1
2.37-2.44	0.956	916	0.782	1.031	1
2.44-2.52	0.776	855	0.81	0.838	1
2.52-2.6	0.603	880	0.866	0.651	1
2.6-2.69	0.525	795	0.893	0.567	1
2.69-2.79	0.432	819	0.933	0.465	1
2.79-2.9	0.323	753	0.957	0.348	1
2.9-3.03	0.245	731	0.976	0.264	1
3.03-3.18	0.183	718	0.987	0.198	1
3.18-3.35	0.142	646	0.99	0.153	1
3.35-3.56	0.106	648	0.993	0.115	1
3.56-3.8	0.088	596	0.995	0.095	1
3.8-4.11	0.063	541	0.997	0.069	1
4.11-4.5	0.047	516	0.998	0.05	1
4.5-5.03	0.047	468	0.998	0.051	1
5.03-5.81	0.053	408	0.998	0.057	1
5.81-7.12	0.049	350	0.998	0.054	1
7.12-10.06	0.04	277	0.999	0.044	1

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0403	refinement
XSCALE		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→38.854 Å / Cor.coef. F_o:F_c: 0.958 / Cor.coef. F_o:F_c free: 0.93 / SU B: 9.577 / SU ML: 0.226 / Cross valid method: FREE R-VALUE / ESU R: 0.45 / ESU R Free: 0.256
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2494	669	5.179 %
R_work	0.1978	12248	-
all	0.201	-	-
obs	-	12917	99.247 %

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: 51.813 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.028 Å²	0 Å²	-0.017 Å²
2-	-	0.04 Å²	-0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→38.854 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2386	0	0	54	2440

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	2424
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2314
X-RAY DIFFRACTION	r_angle_refined_deg	1.085	1.643	3291
X-RAY DIFFRACTION	r_angle_other_deg	0.377	1.569	5317
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.557	5	302
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.26	5	14
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.262	10	423
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.718	10	104
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	401
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	2796
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	548
X-RAY DIFFRACTION	r_nbd_refined	0.197	0.2	446
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.211	0.2	2070
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	1235
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1384
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.155	0.2	84
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.18	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.192	0.2	67
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.111	0.2	5
X-RAY DIFFRACTION	r_mcbond_it	3.705	4.977	1214
X-RAY DIFFRACTION	r_mcbond_other	3.706	4.977	1214
X-RAY DIFFRACTION	r_mcangle_it	5.48	8.936	1514
X-RAY DIFFRACTION	r_mcangle_other	5.478	8.938	1515
X-RAY DIFFRACTION	r_scbond_it	4.965	5.766	1210
X-RAY DIFFRACTION	r_scbond_other	4.964	5.769	1211
X-RAY DIFFRACTION	r_scangle_it	7.68	10.298	1777
X-RAY DIFFRACTION	r_scangle_other	7.678	10.3	1778
X-RAY DIFFRACTION	r_lrange_it	9.821	53.537	2667
X-RAY DIFFRACTION	r_lrange_other	9.826	53.545	2667

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
2.25-2.308	0.322	31	0.309	922	0.309	961	0.925	0.939	99.1675	0.273
2.308-2.371	0.345	51	0.281	847	0.284	905	0.914	0.95	99.2265	0.247
2.371-2.44	0.29	50	0.265	870	0.266	929	0.94	0.956	99.0312	0.23
2.44-2.514	0.287	33	0.247	818	0.249	862	0.95	0.963	98.7239	0.216
2.514-2.597	0.298	45	0.22	833	0.224	880	0.959	0.97	99.7727	0.186
2.597-2.687	0.389	34	0.212	764	0.218	801	0.904	0.973	99.6255	0.184
2.687-2.788	0.225	56	0.226	759	0.226	825	0.965	0.97	98.7879	0.189
2.788-2.901	0.299	48	0.2	689	0.206	743	0.95	0.975	99.1925	0.172
2.901-3.03	0.277	42	0.2	700	0.205	743	0.95	0.976	99.8654	0.182
3.03-3.177	0.28	27	0.203	682	0.205	714	0.952	0.978	99.2997	0.185
3.177-3.347	0.25	31	0.196	623	0.199	659	0.966	0.978	99.2413	0.182
3.347-3.549	0.287	34	0.205	603	0.209	639	0.949	0.979	99.687	0.189
3.549-3.791	0.257	42	0.196	542	0.2	590	0.967	0.982	98.983	0.183
3.791-4.092	0.241	29	0.191	530	0.194	562	0.966	0.983	99.4662	0.182
4.092-4.477	0.245	24	0.151	489	0.156	515	0.966	0.988	99.6116	0.153
4.477-4.998	0.164	14	0.148	454	0.148	471	0.99	0.988	99.3631	0.148
4.998-5.755	0.206	32	0.175	372	0.178	411	0.978	0.982	98.2968	0.17
5.755-7.01	0.201	22	0.198	325	0.198	350	0.979	0.98	99.1429	0.193
7.01-9.756	0.154	15	0.17	270	0.169	285	0.991	0.983	100	0.185
9.756-38.854	0.24	9	0.195	156	0.198	165	0.976	0.978	100	0.218

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