PDB-5t86: Crystal structure of CDI complex from E. coli A0 34/86

ID or keywords:

Entry

Database: PDB / ID: 5t86

Title

Crystal structure of CDI complex from E. coli A0 34/86

Components

CdiA toxin
CdiI immunity protein

Keywords

TOXIN /

Contact-dependent growth inhibition /

antitoxin /

immunity protein /

Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes / UC4CDI

Function / homology

Function and homology information

: /

toxin activity / membrane => GO:0016020 /

cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2 Å

Authors

Michalska, K. / Stols, L. / Jedrzejczak, R. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) / Midwest Center for Structural Genomics (MCSG)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of CDI complex from E. coli A0 34/86
Authors: Michalska, K. / Stols, L. / Jedrzejczak, R. / Hayes, C.S. / Goulding, C.W. / Joachimiak, A. / Structure-Function Analysis of Polymorphic CDI Toxin-Immunity Protein Complexes (UC4CDI) / ...

History

Deposition	Sep 6, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5t86.cif.gz	104.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5t86.ent.gz	86 KB	Display	PDB format
PDBx/mmJSON format	5t86.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/t8/5t86 ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t86	HTTPS FTP

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Related structure data

Related structure data	5t87
Similar structure data	5qa8-4 1og3-d 4s2n-3 5qa9-4 5qad-1 2p1w-d 5qb3-2 5qay-1 3i7j-2 5qai-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC111439 TargetTrack: MCSG-APC111453

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CdiA toxin

I: CdiI immunity protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	57.934, 59.652, 71.074
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	CdiA toxin Mass: 11733.242 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Details: The cloned fragment starts with V3033 of the original sequence. The purified complex was trypsin-treated and the sequence of most likely cleavage product is provided. Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eco1013 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1RPM1
#2: Protein	CdiI immunity protein Mass: 15051.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AGA26_04870 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B0W5A7
#3: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	The protein sequence for this particular strain is not yet in the UNP database

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.63 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 2% tacsimate pH 4.0, 0.1 M Na acetate, 16% PEG3350, cryo 19% glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2015 / Details: mirrors
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 17148 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / R_merge(I) obs: 0.104 / Net I/σ(I): 16.17
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.743 / Mean I/σ(I) obs: 1.94 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing
SBC-Collect		data collection

Refinement

Method to determine structure:

SAD / Resolution: 2→30 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.917 / SU B: 8.826 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23396	799	4.8 %	RANDOM
R_work	0.18278	-	-	-
obs	0.18507	15909	97.43 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 29.68 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.63 Å²	0 Å²	0 Å²
2-	-	-0.17 Å²	0 Å²
3-	-	-	0.8 Å²

Refinement step

Cycle: 1 / Resolution: 2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1794	0	20	106	1920

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	1856
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	1789
X-RAY DIFFRACTION	r_angle_refined_deg	1.562	1.969	2501
X-RAY DIFFRACTION	r_angle_other_deg	0.943	3	4118
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.544	5	226
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.786	24.944	89
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.76	15	322
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.531	15	11
X-RAY DIFFRACTION	r_chiral_restr	0.093	0.2	271
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	2111
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	416
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.681	1.69	915
X-RAY DIFFRACTION	r_mcbond_other	0.659	1.67	909
X-RAY DIFFRACTION	r_mcangle_it	1.064	2.502	1134
X-RAY DIFFRACTION	r_mcangle_other	1.063	2.503	1135
X-RAY DIFFRACTION	r_scbond_it	1.131	1.827	941
X-RAY DIFFRACTION	r_scbond_other	1.131	1.83	942
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.695	2.691	1368
X-RAY DIFFRACTION	r_long_range_B_refined	3.861	20.113	2064
X-RAY DIFFRACTION	r_long_range_B_other	3.86	20.122	2065
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.003→2.111 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.268	103	-
R_work	0.236	1969	-
obs	-	-	84.64 %

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	6.8465	3.2027	0.0702	10.3785	-4.5115	9.1741	-0.7239	1.5985	-0.0021	-1.3441	0.8897	0.1358	0.5706	-0.8909	-0.1658	0.2921	-0.1803	0.0005	0.616	-0.0316	0.0236	25.8078	-4.4478	25.9223
2	10.0971	-0.4557	-0.9254	2.4068	0.0113	2.7369	0.1086	0.1325	0.0546	-0.1688	-0.0504	-0.0226	0.3883	-0.1053	-0.0583	0.1251	-0.0372	0.007	0.1111	-0.0181	0.0874	29.4561	-11.0214	28.2805
3	5.1803	-2.7544	-0.3859	6.5327	2.0914	2.8065	-0.2473	-0.1698	-0.4915	-0.1319	0.1376	-0.4068	0.2569	0.5441	0.1097	0.1851	0.0664	0.0665	0.138	0.0989	0.2029	39.2432	-11.6883	39.3332
4	5.0149	-3.5045	-3.1492	2.4891	2.2277	1.9971	0.1314	0.2126	0.0973	0.01	-0.1445	0.0232	-0.0208	-0.1436	0.0131	0.3898	-0.0398	0.1042	0.2774	-0.0216	0.3702	28.9235	0.9155	48.5547
5	7.3473	0.9912	-3.2699	0.5669	0.5455	4.1086	-0.0018	-0.0003	0.1194	-0.0282	0.0564	-0.0087	0.0911	0.0367	-0.0546	0.0724	-0.0272	0.0226	0.0303	-0.0134	0.0103	36.0127	-2.5937	35.3257
6	11.4712	2.7082	-0.1962	1.7811	-0.7106	1.3727	-0.0949	0.3341	0.0534	-0.1543	0.0619	0.0176	0.0069	-0.0898	0.033	0.0858	0.012	0.0046	0.0542	-0.0018	0.0194	35.7448	-0.6572	27.8452
7	5.7676	-3.7345	0.7421	4.9414	0.7798	9.5981	-0.143	-0.0647	-0.0597	-0.0565	0.0216	0.3281	-0.3509	-0.4786	0.1214	0.0582	-0.0322	-0.0183	0.091	0.0243	0.1207	16.2814	-1.8201	37.0633
8	10.3144	-5.3259	5.2496	11.528	-8.6353	6.6734	0.1479	-0.0776	-0.0937	0.0278	0.1209	0.4001	0.0198	-0.0891	-0.2688	0.1187	-0.0148	0.05	0.0113	0.008	0.0472	22.5593	-9.1944	42.4627
9	3.2813	3.1174	2.5135	11.3782	2.0204	2.7359	0.0934	-0.0991	-0.1119	0.1168	-0.1312	0.0374	0.0951	0.1711	0.0378	0.0425	0.0154	0.0003	0.098	0.0184	0.0639	51.0834	1.7242	43.2742
10	3.2343	-0.9823	-1.072	1.884	-0.9578	3.9776	-0.0434	-0.2674	-0.2291	0.1245	0.1067	0.0322	-0.0512	0.0916	-0.0634	0.0567	0.0199	-0.0163	0.0399	0.0071	0.0351	40.7762	11.1135	53.7745
11	1.5291	2.5945	-0.8586	8.4782	-3.568	1.5908	-0.0788	-0.0337	-0.2958	-0.1084	0.096	-0.1193	0.06	-0.0986	-0.0172	0.1113	-0.0257	0.0378	0.1404	-0.0236	0.1091	25.8932	11.8461	43.214
12	5.4798	-0.553	-2.4744	1.5514	1.0904	8.5781	-0.005	-0.5136	0.4475	0.0274	0.1119	-0.0302	-0.1155	0.0991	-0.107	0.0524	0.008	-0.0108	0.0917	-0.0109	0.0776	28.0565	21.3871	38.9856
13	9.9944	3.1356	1.8483	8.7683	-0.1902	4.2659	0.0574	0.3936	0.2064	-0.4858	-0.0094	-0.2628	0.0106	0.2682	-0.048	0.0338	0.006	0.0227	0.0539	0.021	0.0277	41.7284	19.4035	31.8414
14	8.6084	1.5321	5.5533	8.6425	-3.8405	6.3683	-0.2215	0.6288	0.4424	1.3999	-0.0926	0.0389	-0.9785	0.5275	0.3142	0.2822	-0.0212	0.0239	0.1748	-0.0058	0.173	43.5948	25.5392	43.4009
15	2.4626	-0.9049	-1.005	0.5519	-0.3726	3.2911	-0.0067	-0.1708	0.1606	0.088	0.0693	-0.0583	-0.1482	0.1275	-0.0626	0.082	0.0233	-0.0024	0.0416	0.0006	0.0182	42.4564	10.6371	42.7874
16	3.6875	-1.8888	-2.0847	12.6132	0.4207	5.0295	0.1179	0.1388	0.4759	-0.5139	-0.0255	-0.0706	-0.5272	-0.0961	-0.0924	0.0837	0.0009	-0.0156	0.0375	0.0213	0.0735	35.4281	16.0401	36.3665

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	152 - 161
2	X-RAY DIFFRACTION	2	A	162 - 170
3	X-RAY DIFFRACTION	3	A	171 - 183
4	X-RAY DIFFRACTION	4	A	184 - 193
5	X-RAY DIFFRACTION	5	A	194 - 230
6	X-RAY DIFFRACTION	6	A	231 - 239
7	X-RAY DIFFRACTION	7	A	240 - 245
8	X-RAY DIFFRACTION	8	A	246 - 255
9	X-RAY DIFFRACTION	9	I	2 - 11
10	X-RAY DIFFRACTION	10	I	12 - 33
11	X-RAY DIFFRACTION	11	I	34 - 42
12	X-RAY DIFFRACTION	12	I	43 - 48
13	X-RAY DIFFRACTION	13	I	49 - 59
14	X-RAY DIFFRACTION	14	I	60 - 65
15	X-RAY DIFFRACTION	15	I	66 - 112
16	X-RAY DIFFRACTION	16	I	113 - 124

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