PDB-5e3e: Crystal structure of CdiA-CT/CdiI complex from Y. kristensenii 33638

ID or keywords:

Entry

Database: PDB / ID: 5e3e

Title

Crystal structure of CdiA-CT/CdiI complex from Y. kristensenii 33638

Components

CdiI immunity protein
Large exoprotein involved in heme utilization or adhesion

Keywords

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

Function / homology

: / :

Function and homology information

Biological species

Yersinia kristensenii ATCC 33638 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Michalska, K. / Joachimiak, G. / Jedrzejczak, R. / 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, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM094585	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	5U01GM102318	United States

Citation

Journal: Nucleic Acids Res. / Year: 2017
Title: The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily.
Authors: Batot, G. / Michalska, K. / Ekberg, G. / Irimpan, E.M. / Joachimiak, G. / Jedrzejczak, R. / Babnigg, G. / Hayes, C.S. / Joachimiak, A. / Goulding, C.W.

History

Deposition	Oct 2, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2015	Provider: repository / Type: Initial release
Revision 1.1	Feb 15, 2017	Group: Database references
Revision 1.2	Feb 22, 2017	Group: Structure summary
Revision 1.3	Mar 1, 2017	Group: Structure summary
Revision 1.4	Sep 20, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Oct 4, 2017	Group: Database references / Category: citation / citation_author 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
Revision 1.6	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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Validation report

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Related structure data

Similar structure data	4i8i-d 1im8-2 6z9i-1 4ws8-d 1p1x-1 4wpl-d 6tl1-2 1ha5-2 1dix-d 3zor-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: MCSG-CPX200312

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CdiI immunity protein

B: Large exoprotein involved in heme utilization or adhesion

C: CdiI immunity protein

D: Large exoprotein involved in heme utilization or adhesion

E: CdiI immunity protein

F: Large exoprotein involved in heme utilization or adhesion

hetero molecules

74.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CdiI immunity protein

B: Large exoprotein involved in heme utilization or adhesion

hetero molecules

defined by author&software
24.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: CdiI immunity protein

D: Large exoprotein involved in heme utilization or adhesion

defined by author&software
24.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: CdiI immunity protein

F: Large exoprotein involved in heme utilization or adhesion

hetero molecules

defined by author&software
24.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	48.890, 57.146, 64.302
Angle α, β, γ (deg.)	78.25, 90.21, 79.11
Int Tables number	1
Space group name H-M	P1

#1: Protein	CdiI immunity protein Mass: 12717.746 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The two proteins in the crystal were co-expressed Source: (gene. exp.) Yersinia kristensenii ATCC 33638 (bacteria) Gene: ykris0001_13520 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 - Gold(DE3) / References: UniProt: C4TSS4
#2: Protein	Large exoprotein involved in heme utilization or adhesion Mass: 12163.340 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: The two proteins in the crystal were co-expressed Source: (gene. exp.) Yersinia kristensenii ATCC 33638 (bacteria) Gene: ykris0001_13530 / Plasmid: pMCSG81 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 - Gold(DE3) / References: UniProt: C4TSS5
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 436 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	SEQUENCE IDENTICAL TO UNP REFERENCE C4TSS4 BUT WITH LONGER OPEN READING FRAME AT N-TERMINUS

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.19 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M MgCl2, 0.1 M Na citrate pH 5.0, 15% PEG4000, cryo 20% PEG400

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2014 / Details: Mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97926 Å / Relative weight: 1
Reflection	Resolution: 1.7→30 Å / Num. obs: 71046 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / R_merge(I) obs: 0.082 / Net I/σ(I): 8.13
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.437 / Mean I/σ(I) obs: 2.26 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
PHENIX		refinement
SBC-Collect		data collection
HKL-3000		data scaling
HKL-3000		phasing
HKL-3000		data reduction

Refinement

Method to determine structure:

SAD / Resolution: 1.7→30 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.945 / SU B: 4.388 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20222	1423	2 %	RANDOM
R_work	0.17391	-	-	-
obs	0.17448	69621	96.75 %	-

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: 22.432 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.19 Å²	0.97 Å²	0.44 Å²
2-	-	1 Å²	0.08 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: 1 / Resolution: 1.7→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5015	0	2	436	5453

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	5266
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4894
X-RAY DIFFRACTION	r_angle_refined_deg	1.368	1.973	7161
X-RAY DIFFRACTION	r_angle_other_deg	0.803	3	11311
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.083	5	657
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.578	24.677	248
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.974	15	879
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.545	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	793
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6048
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1187
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	1.044	1.237	2601
X-RAY DIFFRACTION	r_mcbond_other	1.034	1.236	2600
X-RAY DIFFRACTION	r_mcangle_it	1.775	1.842	3267
X-RAY DIFFRACTION	r_mcangle_other	1.776	1.843	3268
X-RAY DIFFRACTION	r_scbond_it	1.486	1.36	2665
X-RAY DIFFRACTION	r_scbond_other	1.486	1.36	2665
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.327	1.981	3894
X-RAY DIFFRACTION	r_long_range_B_refined	5.079	10.384	6394
X-RAY DIFFRACTION	r_long_range_B_other	4.965	9.917	6211
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.701→1.745 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.26	105	-
R_work	0.232	4968	-
obs	-	-	92.51 %

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	3.0285	0.0201	2.8969	3.8233	-0.6026	6.2381	-0.0457	-0.0523	0.0695	-0.0075	-0.0585	-0.2673	-0.2686	-0.0865	0.1042	0.0774	0.0081	-0.0016	0.0168	-0.0007	0.1187	19.1474	82.6016	64.5341
2	0.7716	-0.8437	-0.2587	1.6281	0.6238	0.7188	-0.0178	-0.0238	-0.0624	-0.0216	-0.0106	-0.0266	-0.0491	-0.0283	0.0284	0.0725	-0.0011	0.0177	0.0728	0.0113	0.1277	20.5753	65.7567	62.101
3	0.2229	-0.1581	0.0045	0.4721	-0.1741	0.3014	-0.0205	0.0054	-0.0468	0.0138	0.02	0.0848	-0.0247	-0.0323	0.0005	0.0924	-0.0074	0.022	0.0755	0.0131	0.1126	10.1024	69.0263	61.7469
4	0.7503	-0.6468	0.3626	1.6416	0.2492	1.1481	-0.0485	0.0201	-0.0024	0.0054	0.0451	-0.0035	-0.0565	0.0409	0.0034	0.0725	-0.0091	0.0167	0.0874	0.0113	0.1059	19.1357	73.7574	52.1902
5	0.9567	0.5575	-0.9026	0.4148	-0.2607	3.1455	-0.0196	0.046	-0.0002	-0.0006	0.0931	-0.0075	0.0193	-0.1173	-0.0735	0.0697	-0.0049	0.014	0.1034	0.0079	0.1082	8.4642	66.1962	53.6148
6	1.5829	0.7319	-2.495	2.5727	-2.4714	4.7259	-0.093	-0.0874	-0.0269	-0.0069	0.1608	0.0998	0.1248	0.0324	-0.0679	0.0769	0.0097	0.0064	0.0825	0.0054	0.1447	34.7502	58.4226	63.0355
7	0.6095	0.1601	0.234	0.4974	0.3803	1.1794	-0.0099	-0.0475	-0.0288	-0.026	-0.0075	-0.047	0.0401	0.0091	0.0173	0.0623	-0.0025	0.018	0.091	0.0106	0.1133	36.6103	64.885	58.0323
8	1.0551	-0.2532	-0.1406	0.1206	0.0854	0.0695	0.0105	-0.1569	0.0853	-0.0469	0.0144	-0.0156	-0.0542	0.0169	-0.0249	0.0754	-0.0218	0.024	0.0976	-0.0094	0.1116	30.7819	71.195	66.0373
9	13.6753	0.6359	-1.1172	0.2244	-1.0991	5.7388	-0.2041	-0.3916	-0.5141	-0.1957	0.0411	-0.0505	1.0016	-0.3215	0.163	0.2013	-0.0227	0.0502	0.0922	0.0505	0.0665	25.5586	58.9026	79.6396
10	1.3621	0.3829	-1.797	1.8274	-1.3034	2.878	-0.1644	-0.1348	-0.1034	0.0826	0.0501	-0.0994	0.0484	0.1567	0.1143	0.1159	0.0121	0.0259	0.0917	0.0246	0.119	31.2214	64.4558	69.4139
11	1.2506	-1.4306	0.2817	1.7047	-0.5328	1.445	-0.0031	-0.0307	0.0822	-0.0292	-0.0259	-0.1013	-0.0908	0.1379	0.0289	0.0868	-0.0007	0.0124	0.1047	0.0019	0.0943	54.3795	61.3341	30.332
12	1.5014	-0.5929	-0.7172	3.116	1.2506	1.1824	-0.0701	0.0809	-0.0838	-0.2331	0.0473	0.191	0.1233	-0.2486	0.0228	0.1132	-0.0658	-0.0348	0.1451	0.0215	0.0749	44.467	57.5413	25.572
13	0.3937	-0.0294	1.7475	0.6669	-0.6363	8.1866	0.04	-0.0055	-0.0296	-0.0342	-0.0062	-0.0779	0.2451	0.0162	-0.0338	0.0796	0.0214	0.002	0.0873	0.0087	0.095	57.0817	49.9853	33.2772
14	1.267	-0.9318	0.453	0.8832	0.0974	1.2508	0.0103	0.0104	-0.0172	0.0229	0.0115	-0.004	-0.0375	0.0217	-0.0218	0.0977	-0.0161	0.0069	0.0908	0.0128	0.0866	52.6485	61.8239	41.9874
15	1.3628	-0.1958	-0.571	1.2303	1.4851	3.1457	-0.0059	-0.0367	-0.0668	0.0459	-0.0284	-0.0408	0.2674	-0.1286	0.0344	0.0967	-0.0311	0.0173	0.0646	0.0039	0.0989	46.6753	51.757	38.2132
16	5.7417	-0.1119	2.0933	5.2438	0.6429	5.9605	0.0175	0.3886	0.0218	-0.1153	0.0596	0.2921	-0.1857	0.1053	-0.0771	0.1604	0.0418	0.0076	0.0425	0.0064	0.0334	43.9114	75.3484	22.0635
17	1.2588	0.0107	-1.1851	1.3908	-1.1095	2.3291	0.0888	0.067	-0.0394	0.3094	0.0227	-0.0335	-0.6205	-0.2099	-0.1115	0.3417	0.0928	0.1183	0.0607	0.0515	0.083	46.9061	79.7069	29.6423
18	0.648	0.0474	-0.6676	1.2462	0.0127	1.3489	0.0041	-0.0471	-0.0061	0.0679	0.0112	-0.0058	-0.1167	0.1598	-0.0153	0.1	-0.0183	0.0105	0.1093	0.0086	0.068	60.6147	67.5894	19.1335
19	5.0733	0.4141	-3.1653	2.2776	-1.2114	2.6913	0.3091	-0.2726	0.0081	0.2257	-0.1778	-0.0229	-0.5551	0.2533	-0.1312	0.3342	-0.0641	0.0897	0.0349	-0.0021	0.067	52.6631	80.6852	36.255
20	0.2552	-0.0795	-0.8334	0.163	0.7825	4.8893	0.0412	0.0225	0.0361	-0.0063	-0.0404	0.0024	-0.1718	-0.0966	-0.0008	0.1235	-0.0001	0.0061	0.0799	0.0172	0.0845	52.8447	69.5444	18.3627
21	0.563	-0.6848	-0.4252	2.6679	1.4056	1.0493	-0.028	-0.0398	-0.0044	-0.1354	0.038	-0.0052	-0.0329	-0.1033	-0.0101	0.091	-0.0073	0.0091	0.0584	0.0099	0.1272	38.477	30.7386	59.8843
22	0.8148	-0.5859	-0.0149	1.1891	-1.033	1.4761	-0.0062	-0.031	0.1027	0.0398	0.0293	-0.0101	-0.0253	-0.0369	-0.0231	0.0902	0.0052	0.0052	0.0524	-0.0054	0.134	37.1023	45.389	63.2838
23	0.1438	-0.0404	-0.0885	0.676	-0.3184	0.5978	0.0133	-0.0258	0.0549	-0.0298	-0.0054	0.0092	-0.0372	0.0298	-0.0079	0.0973	0.0018	0.0084	0.0616	0.0161	0.1211	46.7183	35.6513	56.9353
24	0.2209	0.239	0.1346	0.7554	-0.1851	4.0894	0.0157	-0.0712	0.0655	-0.0113	0.037	-0.017	-0.143	0.0641	-0.0527	0.0817	-0.0159	0.0093	0.081	-0.0021	0.1381	51.1538	42.5073	58.8649
25	8.4033	-4.67	3.9274	3.1065	-4.2255	10.0035	-0.0267	-0.1344	0.3086	0.172	-0.0233	-0.145	-0.6334	0.3133	0.05	0.0971	-0.0572	0.0106	0.0658	-0.0538	0.0953	49.9191	44.2975	69.166
26	2.8431	-1.014	-2.5773	0.4901	0.194	6.4396	-0.1981	-0.0371	-0.1587	0.1197	0.0337	0.059	-0.1052	-0.092	0.1644	0.0821	-0.0003	0.0051	0.0542	-0.0323	0.1472	22.785	50.4563	51.7771
27	1.6476	0.6707	0.2096	0.5013	-0.0691	0.1318	-0.06	0.0571	0.0149	-0.0189	0.0479	-0.0146	-0.0139	-0.0157	0.0122	0.0699	-0.017	0.0229	0.0924	-0.0029	0.1355	28.7104	48.8569	44.9791
28	2.8031	-0.2692	1.5492	0.3992	-0.1252	1.246	0.1191	-0.1116	-0.1423	-0.0117	0.0362	0.0111	0.0363	-0.0838	-0.1553	0.0767	-0.0202	-0.0079	0.0513	0.0517	0.1195	21.6507	35.5474	62.6115
29	1.7092	0.6814	1.179	1.5872	0.1404	0.905	0.1187	0.3329	-0.1868	-0.1246	0.0164	-0.0629	0.1474	0.2342	-0.1351	0.0793	-0.0054	0.0215	0.1324	-0.0486	0.0979	27.6966	39.4489	43.1482
30	0.4406	0.0048	-0.0842	0.4524	0.3656	3.8053	0.0225	-0.0693	-0.0971	-0.015	0.0885	-0.0101	-0.0131	-0.0677	-0.111	0.0713	0.0133	-0.0016	0.0695	0.0235	0.1158	23.4334	41.585	60.1916

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 7
2	X-RAY DIFFRACTION	2	A	8 - 26
3	X-RAY DIFFRACTION	3	A	27 - 62
4	X-RAY DIFFRACTION	4	A	63 - 80
5	X-RAY DIFFRACTION	5	A	81 - 99
6	X-RAY DIFFRACTION	6	B	168 - 177
7	X-RAY DIFFRACTION	7	B	178 - 212
8	X-RAY DIFFRACTION	8	B	213 - 263
9	X-RAY DIFFRACTION	9	B	264 - 268
10	X-RAY DIFFRACTION	10	B	269 - 281
11	X-RAY DIFFRACTION	11	C	5 - 22
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16	X-RAY DIFFRACTION	16	D	169 - 175
17	X-RAY DIFFRACTION	17	D	176 - 210
18	X-RAY DIFFRACTION	18	D	211 - 237
19	X-RAY DIFFRACTION	19	D	238 - 258
20	X-RAY DIFFRACTION	20	D	259 - 281
21	X-RAY DIFFRACTION	21	E	1 - 14
22	X-RAY DIFFRACTION	22	E	15 - 44
23	X-RAY DIFFRACTION	23	E	45 - 81
24	X-RAY DIFFRACTION	24	E	82 - 94
25	X-RAY DIFFRACTION	25	E	95 - 99
26	X-RAY DIFFRACTION	26	F	168 - 178
27	X-RAY DIFFRACTION	27	F	179 - 204
28	X-RAY DIFFRACTION	28	F	205 - 232
29	X-RAY DIFFRACTION	29	F	233 - 255
30	X-RAY DIFFRACTION	30	F	256 - 281

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