PDB-3c0n: Crystal structure of the proaerolysin mutant Y221G at 2.2 A

ID or keywords:

Entry

Database: PDB / ID: 3c0n

Title

Crystal structure of the proaerolysin mutant Y221G at 2.2 A

Components

Aerolysin

Keywords

TOXIN / CYTOLYTIC TOXIN / PORE-FORMING TOXIN

Function / homology

Function and homology information

symbiont-mediated cytolysis of host cell / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function

Biological species

Aeromonas hydrophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Pernot, L. / Schiltz, M. / Thurnheer, S. / Burr, S.E. / van der Goot, G.

Citation

Journal: Nat.Chem.Biol. / Year: 2013
Title: Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.
Authors: Degiacomi, M.T. / Iacovache, I. / Pernot, L. / Chami, M. / Kudryashev, M. / Stahlberg, H. / van der Goot, F.G. / Dal Peraro, M.

History

Deposition	Jan 21, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 12, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Oct 2, 2013	Group: Database references
Revision 1.3	Nov 10, 2021	Group: Database references / Category: database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3c0n.cif.gz	364.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3c0n.ent.gz	300.4 KB	Display	PDB format
PDBx/mmJSON format	3c0n.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3c0n_validation.pdf.gz	435.5 KB	Display	wwPDB validaton report
Full document	3c0n_full_validation.pdf.gz	451.7 KB	Display
Data in XML	3c0n_validation.xml.gz	37.2 KB	Display
Data in CIF	3c0n_validation.cif.gz	53.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c0/3c0n ftp://data.pdbj.org/pub/pdb/validation_reports/c0/3c0n	HTTPS FTP

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Related structure data

Related structure data	3c0mSC 3c0oC 1pre S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3g4n-2 3hu6-d 3hqi-d 3g4n-1 6djw-d 4nf9-d 5dhm-d 3kxl-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) 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
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (10) #69 - Sep 2005 Cholera Toxin similarity (4) #232 - Apr 2019 Proteins and Biominerals similarity (1) #134 - Feb 2011 Integrin similarity (1) #75 - Mar 2006 Tissue Factor similarity (1)

Deposited unit

A: Aerolysin

B: Aerolysin

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

1

A: Aerolysin

defined by author&software
51.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Aerolysin

defined by author&software
51.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.360, 89.768, 166.616
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Aerolysin / proaerolysin Mass: 51874.332 Da / Num. of mol.: 2 / Mutation: Y221G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: aerA / Plasmid: pMMB66EH / Production host: Aeromonas salmonicida (bacteria) / Strain (production host): CD3 / References: UniProt: P09167
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.49 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 9-11% PEG 4000, 100mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9536 Å
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 13, 2006
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9536 Å / Relative weight: 1
Reflection	Resolution: 2.2→64.82 Å / Num. all: 54407 / Num. obs: 54407 / % possible obs: 100 % / Redundancy: 21.3 % / R_merge(I) obs: 0.118 / R_sym value: 0.113 / Net I/σ(I): 27.04
Reflection shell	Resolution: 2.2→2.32 Å / Redundancy: 18.2 % / R_merge(I) obs: 0.527 / Mean I/σ(I) obs: 7.98 / Num. unique all: 142371 / R_sym value: 0.498 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.3.0008	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3C0M

3c0m

Resolution: 2.2→64.82 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.918 / SU B: 10.076 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.203 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23828	2755	5.1 %	RANDOM
R_work	0.18918	-	-	-
obs	0.19164	54335	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 19.383 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	0 Å²
2-	-	0.16 Å²	0 Å²
3-	-	-	0.04 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.36 Å	0.3 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.29 Å	0.26 Å

Refinement step

Cycle: LAST / Resolution: 2.2→64.82 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7039	0	0	417	7456

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	7239
X-RAY DIFFRACTION	r_angle_refined_deg	1.727	1.931	9884
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.859	5	896
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.778	24.561	342
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.094	15	1104
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.236	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.118	0.2	1043
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5672
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	3035
X-RAY DIFFRACTION	r_nbtor_refined	0.313	0.2	4771
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	486
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.205	0.2	55
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.162	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	1.098	1.5	4576
X-RAY DIFFRACTION	r_mcangle_it	1.78	2	7198
X-RAY DIFFRACTION	r_scbond_it	2.873	3	3196
X-RAY DIFFRACTION	r_scangle_it	4.39	4.5	2686

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.238	208	-
R_work	0.192	3708	-
obs	-	-	99.95 %

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	2.3695	0.8626	-0.1034	5.3506	3.3789	7.8984	0.0893	-0.0658	0.3145	0.0267	0.0569	-0.218	-0.1556	0.3131	-0.1463	0.097	0.0017	0.0166	0.0812	0.0169	0.1256	29.0265	-5.3297	-0.4447
2	0.2121	-0.0544	-0.225	0.6835	0.7364	1.0296	0.0223	-0.0836	0.0221	0.007	-0.0091	-0.0095	-0.0459	0.0642	-0.0132	0.0871	-0.0137	0.0066	0.0792	0.0071	0.0633	26.7712	-7.5234	11.5549
3	3.8354	0.8411	0.0581	2.7812	-0.6897	3.425	0.0373	-0.3119	0.6494	0.0985	0.0122	0.2902	-0.4524	0.0218	-0.0496	0.0856	-0.0489	0.0172	0.0555	-0.1021	0.1374	29.1791	27.246	26.3351
4	2.2618	1.64	0.3837	4.1663	-0.4121	0.6868	0.0754	-0.176	0.0151	0.116	0.0448	0.3092	0.0614	-0.1306	-0.1202	0.1745	0.0339	0.0715	0.2076	-0.0979	0.098	13.4144	4.5069	31.3735
5	1.6381	1.772	3.3034	3.1594	4.7291	11.6791	0.1686	-0.1897	-0.1092	0.2171	-0.2631	0.1783	0.5864	-0.712	0.0945	0.0148	-0.0565	0.0354	0.0521	-0.0183	0.0613	-14.0763	-35.336	24.3994
6	3.2963	2.9092	0.0681	4.3134	-0.5578	1.2324	0.1913	-0.0644	0.2028	-0.0489	-0.1491	0.11	-0.0444	0.0502	-0.0421	0.1169	0.0334	0.0456	0.1197	-0.0724	0.1093	0.971	-0.229	33.8367
7	4.7513	0.8292	0.6833	0.4042	1.0915	3.7407	0.2783	0.0357	-0.2714	-0.1353	-0.0528	0.266	0.3729	-0.0946	-0.2255	0.0714	0.0089	-0.0344	0.054	-0.0687	0.0677	1.2965	-4.824	30.5645
8	1.8363	0.5323	2.0588	3.0707	3.7029	5.6163	0.1038	-0.1228	0.0267	0.0972	-0.1689	0.0996	0.3068	-0.029	0.0651	0.1009	-0.0207	0.0125	0.0826	-0.0074	0.0989	-9.9912	-32.505	25.9137
9	1.8773	2.4727	-1.2946	6.0252	-3.1139	2.7818	-0.058	-0.0249	0.0275	-0.1171	-0.1217	-0.2712	-0.0641	0.0765	0.1797	0.1098	0.0347	-0.0046	0.1473	-0.0505	0.1735	16.4963	10.119	27.0313
10	2.0195	0.3239	-0.1373	1.2848	0.2535	1.3611	-0.1087	0.2512	0.2121	-0.2814	0.0689	0.0682	-0.115	0.0368	0.0398	0.0933	-0.0458	-0.0163	0.0218	0.0262	0.0418	26.9149	17.9701	10.5152
11	1.0229	1.1877	0.547	2.9035	1.2924	1.7378	0.2101	-0.0416	-0.0454	0.5112	-0.1112	0.2141	0.4293	-0.046	-0.0989	0.1348	0.0218	-0.0113	0.1058	0.0019	0.1262	-3.3675	-21.9623	32.2477
12	1.7825	-0.2458	-0.4098	2.2919	2.361	10.2733	-0.2086	0.0528	-0.257	0.1067	-0.2467	0.2562	0.1126	-0.8824	0.4554	0.047	0.005	0.0281	0.0915	-0.0177	0.1255	-17.6357	-25.5799	30.3563
13	4.2241	1.271	-4.0669	3.5259	-3.2379	6.2167	0.0227	0.2077	0.0532	-0.1388	0.0745	0.209	0.0273	-0.1808	-0.0972	0.0802	-0.045	-0.0493	0.0996	-0.009	0.1085	10.7675	-12.6638	-0.5922
14	2.5563	1.8421	0.7334	2.9417	0.6732	2.1198	-0.1669	-0.0856	0.3627	-0.2048	0.0737	0.3897	-0.2245	-0.1106	0.0933	0.0353	0.01	-0.047	0.0406	0.0057	0.1109	10.1197	-3.9681	2.4283
15	0.4147	0.1266	0.1019	0.4039	-0.0584	0.941	-0.0217	-0.0615	-0.0577	0.0389	0.0075	0.0362	0.0404	0.0619	0.0142	0.0684	-0.0039	-0.01	0.0907	0.0349	0.0936	9.8139	-32.8999	30.5851
16	2.0822	1.5996	-0.0288	5.0099	-0.1791	0.7457	-0.008	-0.0643	0.0591	0.0387	-0.0294	-0.1277	-0.0547	0.0469	0.0374	0.2044	0.0219	-0.022	0.2839	0.032	0.1092	19.6075	-23.0803	31.4546
17	3.6302	1.2648	-0.0363	6.4998	-2.265	5.9368	-0.0123	0.4672	0.1965	-0.6485	0.0904	-0.0566	-0.297	0.57	-0.0781	0.1632	-0.1052	0.031	0.2179	-0.0505	0.0368	50.6511	19.8772	21.8458
18	3.4874	3.5524	-1.8449	4.9074	-0.9713	3.836	0.106	-0.0424	-0.0235	0.2569	-0.0235	-0.3117	0.0873	0.1759	-0.0825	0.0322	0.0216	-0.0476	0.1425	0.0374	0.1401	33.4306	-13.5872	36.0675
19	2.6791	0.4989	0.0359	3.6786	-0.2443	2.8636	-0.0246	0.1728	0.2879	-0.1808	0.0834	-0.5993	-0.2741	0.3552	-0.0588	-0.0187	-0.0827	0.0207	0.1034	0.0203	0.0759	36.7857	-7.1568	30.6796
20	3.8797	1.1381	1.3034	7.3867	0.0664	7.29	-0.1586	0.4711	-0.0578	-0.3847	0.2607	0.1113	-0.5465	0.4308	-0.1021	0.1306	-0.131	0.0188	0.2092	-0.0719	0.094	47.877	22.0882	19.5589
21	0.889	1.0049	-0.0108	2.1219	0.154	0.2999	0.0277	-0.0688	0.034	0.0912	-0.0189	0.0133	0.0007	0.0536	-0.0088	0.1133	0.0183	-0.0033	0.1567	0.0301	0.1012	24.4321	-16.2661	30.6681
22	1.1177	-0.0627	-0.0661	0.669	-0.4429	1.9701	0.0249	0.0779	-0.1182	-0.1805	0.0016	0.046	0.1963	0.0785	-0.0265	0.114	-0.0061	-0.0254	0.0502	-0.0048	0.0489	10.2502	-35.9898	12.82
23	0.8017	0.6515	0.0106	1.732	0.188	0.502	0.0374	-0.1437	0.059	0.1037	-0.0604	-0.022	-0.0616	0.0009	0.023	0.1745	-0.0149	-0.0248	0.2012	0.0125	0.148	26.6004	-8.6986	32.1354
24	2.2978	0.1272	0.7914	3.2508	-1.3534	4.3297	-0.1435	0.3987	0.0711	-0.4253	0.1082	-0.2404	-0.1511	0.5279	0.0353	0.0747	-0.1025	0.0397	0.1251	-0.0824	0.0184	52.5713	17.1972	25.9198

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	2 - 23	2 - 23
2	X-RAY DIFFRACTION	2	A	A	24 - 103	24 - 103
3	X-RAY DIFFRACTION	3	A	A	104 - 164	104 - 164
4	X-RAY DIFFRACTION	4	A	A	165 - 195	165 - 195
5	X-RAY DIFFRACTION	5	A	A	196 - 219	196 - 219
6	X-RAY DIFFRACTION	6	A	A	220 - 242	220 - 242
7	X-RAY DIFFRACTION	7	A	A	243 - 274	243 - 274
8	X-RAY DIFFRACTION	8	A	A	275 - 298	275 - 298
9	X-RAY DIFFRACTION	9	A	A	299 - 324	299 - 324
10	X-RAY DIFFRACTION	10	A	A	325 - 397	325 - 397
11	X-RAY DIFFRACTION	11	A	A	398 - 441	398 - 441
12	X-RAY DIFFRACTION	12	A	A	442 - 468	442 - 468
13	X-RAY DIFFRACTION	13	B	B	1 - 21	1 - 21
14	X-RAY DIFFRACTION	14	B	B	22 - 79	22 - 79
15	X-RAY DIFFRACTION	15	B	B	80 - 158	80 - 158
16	X-RAY DIFFRACTION	16	B	B	159 - 194	159 - 194
17	X-RAY DIFFRACTION	17	B	B	195 - 222	195 - 222
18	X-RAY DIFFRACTION	18	B	B	223 - 242	223 - 242
19	X-RAY DIFFRACTION	19	B	B	243 - 276	243 - 276
20	X-RAY DIFFRACTION	20	B	B	277 - 295	277 - 295
21	X-RAY DIFFRACTION	21	B	B	296 - 323	296 - 323
22	X-RAY DIFFRACTION	22	B	B	324 - 390	324 - 390
23	X-RAY DIFFRACTION	23	B	B	391 - 413	391 - 413
24	X-RAY DIFFRACTION	24	B	B	414 - 468	414 - 468

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