PDB-4zqu: CdiA-CT/CdiI toxin and immunity complex from Yersinia pseudotuber...

ID or keywords:

Entry

Database: PDB / ID: 4zqu

Title

CdiA-CT/CdiI toxin and immunity complex from Yersinia pseudotuberculosis

Components

CdiA-CT toxin, Conserved domain protein
CdiI toxin

Keywords

TOXIN / immunity / complex / endonuclease

Function / homology

Function and homology information

deoxyribonuclease I activity / toxin activity / Hydrolases; Acting on ester bonds
Similarity search - Function

Biological species

Yersinia pseudotuberculosis serotype O:3

Salmonella enterica subsp. enterica serovar Rubislaw str. ATCC 10717 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.09 Å

Authors

Morse, R.P. / Johnson, P.M. / Credali, A. / Goulding, C.W.

Funding support

United States, 1items

Citation

Journal: J.Mol.Biol. / Year: 2015
Title: Diversification of beta-Augmentation Interactions between CDI Toxin/Immunity Proteins.
Authors: Morse, R.P. / Willett, J.L. / Johnson, P.M. / Zheng, J. / Credali, A. / Iniguez, A. / Nowick, J.S. / Hayes, C.S. / Goulding, C.W.

History

Deposition	May 11, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 28, 2015	Provider: repository / Type: Initial release
Revision 1.1	Dec 2, 2015	Group: Database references
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_audit_support / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zqu.cif.gz	135.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4zqu.ent.gz	104.9 KB	Display	PDB format
PDBx/mmJSON format	4zqu.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/zq/4zqu ftp://data.pdbj.org/pub/pdb/validation_reports/zq/4zqu	HTTPS FTP

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Related structure data

Related structure data	4zqvC 4zqwC 4g6uS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6hom-2 4hn2-d 4h0n-2 6hon-1 4h0n-3 4mx3-2 3t9d-d 3t9c-d 2rkh-1 1jwa-d Search similar-shape structures by Omokage search (details) 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

A: CdiA-CT toxin, Conserved domain protein

B: CdiI toxin

hetero molecules

34.8 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)	63.510, 68.310, 71.419
Angle α, β, γ (deg.)	90.00, 92.18, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	CdiA-CT toxin, Conserved domain protein Mass: 13692.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis serotype O:3 (strain YPIII) (bacteria) Strain: YPIII / Gene: YPK_0575 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A7FE33, UniProt: A0A0H3B0B8*PLUS
#2: Protein	CdiI toxin Mass: 21023.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Rubislaw str. ATCC 10717 (bacteria) Gene: SEERU717_10215 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R4I987*PLUS
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.83 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 50 mM HEPES, pH 7, 20% PEG 3350, 1% tryptone

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.09→46.49 Å / Num. obs: 18152 / % possible obs: 99.4 % / Redundancy: 3.5 % / Net I/σ(I): 10

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4G6U

4g6u

Resolution: 2.09→46.49 Å / Cross valid method: NONE / σ(F): 1.96 / Phase error: 30.18 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.2566	1851	10.2 %
R_work	0.2054	-	-
obs	0.2112	18149	99.33 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.09→46.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2302	0	2	148	2452

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	2356
X-RAY DIFFRACTION	f_angle_d	0.694	3207
X-RAY DIFFRACTION	f_dihedral_angle_d	13.29	852
X-RAY DIFFRACTION	f_chiral_restr	0.028	372
X-RAY DIFFRACTION	f_plane_restr	0.003	408

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 (%)
2.0872-2.1436	0.3587	143	0.2975	1257	X-RAY DIFFRACTION	88
2.1436-2.2066	0.3065	136	0.2834	1253	X-RAY DIFFRACTION	90
2.2066-2.2778	0.324	126	0.2659	1246	X-RAY DIFFRACTION	90
2.2778-2.3592	0.2712	147	0.2675	1254	X-RAY DIFFRACTION	89
2.3592-2.4536	0.3397	148	0.2637	1239	X-RAY DIFFRACTION	89
2.4536-2.5653	0.3392	134	0.2591	1256	X-RAY DIFFRACTION	90
2.5653-2.7004	0.3062	137	0.2589	1252	X-RAY DIFFRACTION	90
2.7004-2.8695	0.3068	148	0.2454	1258	X-RAY DIFFRACTION	89
2.8695-3.0909	0.2584	144	0.2311	1250	X-RAY DIFFRACTION	89
3.0909-3.4016	0.2641	135	0.2146	1258	X-RAY DIFFRACTION	90
3.4016-3.8929	0.2424	138	0.1779	1269	X-RAY DIFFRACTION	90
3.8929-4.9015	0.1861	137	0.1445	1254	X-RAY DIFFRACTION	89

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	7.2267	1.7048	0.9887	5.9866	-2.1211	3.995	0.1872	-0.3723	-0.2038	-0.0254	-0.5343	-0.4152	-0.1897	0.158	0.2467	0.3767	0.0591	-0.051	0.2143	-0.0875	0.3802	-6.6801	13.5193	11.3905
2	1.5508	-0.8874	0.8154	2.6302	-0.348	3.5997	0.1237	-0.2067	-0.123	-0.2788	0.4263	0.2791	0.7554	0.0692	-0.3407	0.4397	0.0219	-0.1174	0.2752	0.01	0.3138	-10.2609	22.3697	15.7953
3	1.384	-1.3581	0.4035	3.7603	1.005	1.6511	-0.0576	0.0737	-0.2705	0.2435	0.0146	0.6469	0.0622	-0.3024	0.0844	0.3093	0.0033	-0.0152	0.2709	0.0072	0.2753	-16.3811	20.6426	13.5749
4	4.313	0.1558	0.9607	1.5923	0.3996	1.7451	0.2773	-0.718	0.0133	0.3846	-0.1749	-0.3438	0.5465	-0.0196	-0.1223	0.6069	-0.018	0.05	0.3718	-0.0356	0.3412	-18.1702	-3.3543	16.6267
5	1.309	-0.8166	0.2884	4.3522	-0.0587	0.993	-0.0546	-0.4789	0.4453	0.5697	-0.1487	0.8898	-0.0809	0.3139	0.1037	0.3783	-0.0684	0.0973	0.2488	-0.0677	0.4214	-25.7071	7.9477	15.261
6	1.1968	0.0428	-0.2179	1.4203	0.4497	2.0747	-0.0237	-0.0287	-0.3497	0.1502	-0.1164	0.5821	-0.2099	-0.0427	0.1102	0.2885	0.0457	-0.0063	0.3066	0.0535	0.4187	-22.6105	26.9603	18.2947
7	1.8656	0.6471	0.1023	3.8994	-0.4737	1.3275	-0.1172	0.1015	-0.3694	-0.4001	0.1857	0.3522	0.1933	0.201	-0.0936	0.3471	0.0077	-0.02	0.2519	-0.0318	0.3056	-16.2423	6.4221	8.8114
8	3.1604	-1.4017	-0.0021	6.0533	-0.1067	2.6052	-0.1543	-0.1668	0.2757	-0.3828	-0.0291	0.9857	0.3398	-0.3503	0.1164	0.3851	-0.0882	-0.0208	0.2752	-0.0733	0.4223	-25.3402	2.8422	6.1871
9	6.6097	1.9402	1.5757	2.7095	-0.6037	5.3731	-0.0477	0.9286	-0.1598	-0.5178	-0.1037	0.4107	-0.1695	0.5376	0.2216	0.3526	-0.0231	-0.0044	0.2837	0.0022	0.3225	-18.1997	9.1039	6.1259
10	2.4788	0.553	-0.6416	2.2936	0.1985	1.0255	0.1302	-0.307	0.2094	0.0559	-0.0593	0.1285	-0.1843	0.0756	-0.1287	0.2447	0.0619	-0.0153	0.2772	-0.0257	0.2753	-17.338	37.3677	24.3456
11	0.7168	-0.7245	-1.4166	0.7588	1.4657	2.8409	-0.273	-1.1479	0.6782	0.3047	0.0984	-0.3177	-0.5252	0.0351	-0.6365	0.3622	0.1392	-0.0468	0.6824	-0.2646	0.4189	-20.8816	46.6038	32.6705
12	2.3451	-0.0456	-0.3324	1.8682	0.1016	2.8927	0.1536	0.0651	0.4817	-0.1527	-0.1268	-0.1012	-0.1021	0.0387	-0.0477	0.3265	0.0266	0.0096	0.2424	-0.016	0.2867	-9.4321	36.3351	10.249
13	0.9721	0.6529	0.4226	2.2632	-0.0633	4.3294	-0.0299	-0.7274	-0.1937	0.5299	-0.1769	-0.0969	0.5355	0.5495	0.0734	0.3394	0.0379	-0.0286	0.5435	0.0352	0.2267	-8.4662	30.2862	32.813
14	2.0068	-2.0442	0.5472	2.9016	0.0796	2.996	-0.0857	-0.8129	-0.3412	0.6733	0.3992	0.6223	0.0548	-0.4031	-0.2284	0.3901	-0.0188	0.0667	0.5265	0.0985	0.3842	-20.2573	30.152	35.3685
15	2.1652	-2.0457	0.8398	5.0861	-0.2886	1.8372	0.2053	-0.3817	-0.557	0.0014	-0.1396	0.763	0.3375	-0.1829	-0.0674	0.2972	-0.0572	0.0027	0.3758	0.0569	0.4601	-25.7246	31.8664	24.8144
16	0.9025	-0.5734	-0.3941	0.8636	1.1314	1.7275	0.3207	0.8976	-0.858	-0.1952	-0.6138	0.737	1.0182	-1.4252	0.2301	0.5016	-0.139	-0.047	0.6835	-0.1111	0.9564	-34.6171	30.6212	21.8601
17	2.5487	-0.4927	0.0435	3.9404	1.3314	1.8673	-0.2834	-0.3857	-0.0407	0.0276	0.104	0.5416	-0.1399	-0.5216	0.2394	0.2597	0.0575	-0.0233	0.4728	-0.1187	0.4849	-30.9	43.7904	26.9907

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 174 through 183 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 184 through 193 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 194 through 212 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 213 through 225 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 226 through 239 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 240 through 257 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 258 through 270 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 271 through 286 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 287 through 297 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 3 through 37 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 38 through 59 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 60 through 86 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 87 through 105 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 106 through 124 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 125 through 143 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 144 through 152 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 153 through 176 )

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