PDB-3c0o: Crystal structure of the proaerolysin mutant Y221G complexed with...

ID or keywords:

Entry

Database: PDB / ID: 3c0o

Title

Crystal structure of the proaerolysin mutant Y221G complexed with mannose-6-phosphate

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: 2.5 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	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4	Nov 10, 2021	Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5	Nov 1, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	3c0o_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	3c0o_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3c0o_validation.xml.gz	36.9 KB	Display
Data in CIF	3c0o_validation.cif.gz	51.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c0/3c0o ftp://data.pdbj.org/pub/pdb/validation_reports/c0/3c0o	HTTPS FTP

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Related structure data

Related structure data	3c0mC 3c0nSC 1pre C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3c0m-d 3c0n-d 3g4o-d 1z52-d 1z9o-d 1pre-d 4ga5-2 4ga5-4 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

hetero molecules

104 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)	70.954, 90.780, 165.805
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: Chemical

ChemComp-ACT / ACETATE ION

Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂

#3: Sugar

ChemComp-M6P / 6-O-phosphono-alpha-D-mannopyranose / ALPHA-D-MANNOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-mannose / 6-O-phosphono-D-mannose / 6-O-phosphono-mannose

Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₃O₉P

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.57 Å³/Da / Density % sol: 52.2 %
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: 0.979 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 27, 2007
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.5→61.2 Å / Num. all: 37597 / Num. obs: 37597 / % possible obs: 99.3 % / Redundancy: 4.8 % / R_merge(I) obs: 0.094 / R_sym value: 0.076 / Net I/σ(I): 14.01
Reflection shell	Resolution: 2.5→2.64 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.389 / Mean I/σ(I) obs: 4.1 / Num. unique all: 5385 / R_sym value: 0.31 / % possible all: 98.7

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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: 3C0N

3c0n

Resolution: 2.5→61.2 Å / Cor.coef. F_o:F_c: 0.938 / Cor.coef. F_o:F_c free: 0.887 / SU B: 19.495 / SU ML: 0.218 / Cross valid method: THROUGHOUT / ESU R: 0.541 / ESU R Free: 0.315 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27377	1870	5 %	RANDOM
R_work	0.20314	-	-	-
obs	0.20658	37534	99.14 %	-

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: 23.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.13 Å²	0 Å²	0 Å²
2-	-	0.28 Å²	0 Å²
3-	-	-	-0.15 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.46 Å	0.35 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	0.4 Å	0.33 Å

Refinement step

Cycle: LAST / Resolution: 2.5→61.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7038	0	36	173	7247

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	7273
X-RAY DIFFRACTION	r_angle_refined_deg	2.005	1.936	9933
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.241	5	896
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.379	24.561	342
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.178	15	1104
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.909	15	38
X-RAY DIFFRACTION	r_chiral_restr	0.121	0.2	1052
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5676
X-RAY DIFFRACTION	r_nbd_refined	0.259	0.3	3259
X-RAY DIFFRACTION	r_nbtor_refined	0.342	0.5	4899
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.221	0.5	535
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.24	0.3	53
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.133	0.5	12
X-RAY DIFFRACTION	r_mcbond_it	1.581	2	4539
X-RAY DIFFRACTION	r_mcangle_it	2.488	3	7198
X-RAY DIFFRACTION	r_scbond_it	1.664	2	3228
X-RAY DIFFRACTION	r_scangle_it	2.48	3	2735

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.402	140	-
R_work	0.317	2599	-
obs	-	2599	98.85 %

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	12.8052	11.1636	6.9051	28.1346	17.0938	27.7388	0.2613	0.2437	1.1873	-0.0832	0.0919	-0.0392	-0.3586	0.3853	-0.3532	0.1213	-0.0016	0.1055	0.0475	0.0074	0.1538	30.552	-2.342	5.906
2	6.417	-1.6497	4.3495	4.8866	-1.5809	8.7845	0.3774	0.2847	-0.0257	-0.6622	-0.3848	-0.5236	0.1309	0.2298	0.0074	0.1528	0.0424	0.1144	-0.0384	-0.0167	0.1074	30.839	-10.484	-1.517
3	2.3924	0.1901	-0.66	4.2753	0.3925	1.809	0.0588	-0.0199	-0.0784	-0.3786	-0.1013	-0.0228	-0.0775	0.1074	0.0425	0.1053	0.0226	0.0049	0.0496	-0.0097	0.0633	26.624	-15.629	4.442
4	3.864	-2.4008	-8.2113	5.73	7.6395	22.6171	-0.6774	-0.2142	-0.5644	0.3089	-0.0641	0.2141	1.3817	-0.1662	0.7415	0.1079	-0.0691	0.0114	0.0225	0.0399	0.1688	26.629	6.337	21.55
5	28.9757	9.5476	-10.3243	7.0617	-2.2078	4.0428	0.0285	-0.724	-0.4473	0.5154	-0.2957	0.2659	-0.1046	0.4963	0.2671	0.1282	-0.0771	0.0723	0.0746	0.0177	0.0553	19.087	17.658	33.723
6	1.7456	0.4191	-0.3128	4.9795	-1.3939	4.8638	0.1926	-0.262	0.2841	0.3002	-0.121	0.1699	-0.7674	0.08	-0.0716	0.1989	-0.1178	-0.0088	0.0119	-0.0325	0.054	29.932	28.691	24.125
7	2.0841	3.3635	-1.142	8.5049	-2.2254	2.4374	-0.023	-0.1578	0.1084	-0.0749	-0.0198	0.3581	0.0714	-0.2114	0.0428	0.1235	-0.0013	0.0692	0.1815	-0.0038	0.2418	15.496	9.154	28.517
8	2.3866	3.1315	3.6076	9.5935	4.903	9.3132	0.1161	-0.1672	-0.0133	-0.203	-0.4015	0.3909	-0.1721	-0.3576	0.2854	-0.0639	0.0192	0.068	0.008	-0.1044	0.1221	-11.885	-30.306	28.593
9	7.6251	6.4291	-1.7379	12.5967	-3.138	5.5273	0.3514	-0.2625	0.6266	0.0504	-0.0867	1.0862	-0.2807	0.1074	-0.2647	0.0099	0.0235	0.0714	0.0297	-0.0135	0.2146	4.343	2.589	31.16
10	4.9121	3.5926	-1.1716	2.663	-0.7159	0.8391	-0.2297	0.3979	0.4562	-0.5227	0.4112	0.7007	0.7866	0.073	-0.1814	0.2991	-0.0635	0.006	-0.0081	-0.1055	0.2938	-1.109	-6.781	30.208
11	3.5035	1.6385	2.2062	10.609	11.9712	13.5475	0.4638	-0.0924	-0.2889	-0.0995	-0.4231	0.3757	0.2221	-0.4733	-0.0407	0.1695	-0.0364	-0.0578	0.0441	0.0075	0.0892	-10.416	-35.942	26.659
12	3.0189	4.5489	-2.5552	7.3255	-4.3981	3.5329	0.0807	-0.1246	0.262	-0.002	-0.0837	0.4468	-0.1318	0.0692	0.003	0.0568	-0.0341	0.041	0.024	0.0081	0.1093	20.972	16.805	18.933
13	2.709	0.5957	-0.1624	3.0602	0.3571	2.7543	-0.1607	0.1411	-0.2137	-0.5472	0.1204	0.2042	0.0917	0.1277	0.0403	0.1413	-0.0944	0.0059	-0.0215	-0.0132	0.1	26.851	15.451	10.248
14	4.8079	7.255	1.899	13.4256	2.8564	1.7569	0.5017	-0.3082	0.1875	0.6173	-0.5334	0.5133	0.4564	-0.0413	0.0317	0.1672	-0.0028	0.0889	0.0787	-0.0034	0.1653	-4.591	-22.789	31.813
15	1.215	-0.9365	3.5628	3.8918	2.4203	18.8668	-0.3435	-0.1722	-0.0135	-0.263	-0.1326	0.4855	-0.4789	-0.7889	0.4761	0.0064	0.0238	0.0348	0.0507	-0.1517	0.1289	-17.733	-25.411	31.919
16	5.1166	3.627	-7.4783	8.0498	-6.8458	17.0734	-0.1143	0.3391	-0.0611	-0.4129	0.0512	0.2823	-0.1126	-0.3524	0.0631	0.1157	0.0232	-0.1128	0.0383	-0.0277	0.1683	10.786	-13.317	-1.433
17	1.677	0.8828	0.3907	4.6252	-0.5207	2.203	-0.1585	-0.1026	0.2301	-0.155	0.0157	0.3206	-0.385	-0.1116	0.1428	0.109	0.0225	-0.0883	0.0208	-0.0102	0.1257	9.719	-4.552	2.593
18	5.5835	1.0697	2.5907	0.8165	1.3909	2.5105	-0.1067	-0.0832	0.2528	-0.0191	-0.1488	0.0988	-0.2893	0.5071	0.2556	0.0811	0.01	-0.0335	0.0951	-0.0065	0.0215	15.956	-21.576	33.031
19	2.9472	0.3856	0.3355	4.2466	1.1697	0.3402	0.1451	-0.3029	-0.1848	0.3212	-0.0162	0.2924	0.1652	-0.1609	-0.1289	0.0873	0.0107	-0.0092	0.0859	0.0773	0.1442	5.365	-35.444	29.925
20	18.2975	5.8378	-2.5427	4.7703	2.7839	9.2252	0.1749	0.087	-0.3911	0.4848	0.0589	-0.185	0.7833	0.0591	-0.2338	0.1749	0.1255	0.0114	0.1268	0.0712	0.036	13.482	-38.648	36.546
21	4.6996	5.0078	0.7853	11.9201	1.3322	2.1652	-0.0085	-0.2685	-0.0601	0.4018	0.0207	0.0177	0.1415	0.1585	-0.0121	0.1488	0.0686	-0.0049	0.2893	0.054	0.0554	18.088	-25.841	31.405
22	5.165	-0.2844	0.482	12.7916	-3.7271	4.4299	-0.0464	0.569	0.0126	-1.9173	0.0149	-0.529	0.2168	-0.2353	0.0314	0.3515	-0.0758	0.0203	0.1686	-0.1064	-0.0754	49.317	19.38	22.977
23	5.3598	3.9206	-1.0627	6.5738	-0.9307	5.1216	0.2057	-0.2153	0.1396	0.1707	-0.1717	-0.2642	-0.2415	0.4633	-0.034	-0.004	-0.0478	-0.0865	0.2085	0.0227	0.0611	32.504	-10.019	32.853
24	4.3572	6.091	-1.1656	10.1482	-0.7717	0.7622	-0.2125	-0.3276	-0.0065	-1.0528	0.1255	0.4725	-0.5589	0.1148	0.087	0.303	-0.1526	-0.1083	0.2628	0.0337	0.1254	40.93	-0.762	27.212
25	8.3295	13.6221	-7.7722	38.2111	-24.6573	26.3848	-0.4391	0.5072	0.2005	-1.3763	0.4963	-0.5376	0.5677	-0.0684	-0.0573	0.151	-0.0547	-0.0529	0.1923	-0.0613	0.0393	46.887	22.807	25.108
26	1.9539	2.9017	1.4986	7.5547	3.2631	3.0012	-0.0609	-0.1484	0.0626	-0.0512	-0.0531	0.3655	0.0305	0.1482	0.114	0.072	0.0477	-0.0189	0.1546	0.0148	0.1567	16.962	-28.216	25.29
27	3.2667	0.6051	0.1849	1.8926	-0.8131	2.4019	0.0739	0.0627	-0.0003	-0.2624	-0.0068	0.0263	0.3911	0.0013	-0.0671	0.1507	0.0373	-0.0511	0.025	-0.0236	0.0857	10.353	-34.43	13.383
28	2.5589	3.5264	-0.6855	5.7823	-0.4895	0.4083	0.0324	-0.2078	0.2363	-0.1046	-0.141	0.1747	-0.351	0.1495	0.1086	0.2093	-0.0825	-0.1136	0.2206	-0.0151	0.1405	33.144	2.936	28.095
29	4.2418	0.0552	-2.4867	7.0472	-3.7694	10.2755	-0.005	0.4539	0.1575	0.0345	-0.3237	-0.8606	-0.1233	0.4347	0.3287	0.0415	-0.0226	0.0209	0.1841	-0.0263	0.0616	55.027	14.927	31.345
30	13.0807	-18.6381	-10.4747	26.5564	14.9248	8.3878	-1.9995	0.3285	2.4559	-1.9127	-2.939	-0.8621	-0.7436	-1.321	4.9385	0.3475	-0.0043	0.0006	0.342	-0.0032	0.3489	53.598	15.114	15.003

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 - 10	2 - 10
2	X-RAY DIFFRACTION	2	A	A	11 - 33	11 - 33
3	X-RAY DIFFRACTION	3	A	A	34 - 80	34 - 80
4	X-RAY DIFFRACTION	4	A	A	81 - 95	81 - 95
5	X-RAY DIFFRACTION	5	A	A	96 - 109	96 - 109
6	X-RAY DIFFRACTION	6	A	A	110 - 164	110 - 164
7	X-RAY DIFFRACTION	7	A	A	165 - 191	165 - 191
8	X-RAY DIFFRACTION	8	A	A	192 - 225	192 - 225
9	X-RAY DIFFRACTION	9	A	A	226 - 247	226 - 247
10	X-RAY DIFFRACTION	10	A	A	248 - 279	248 - 279
11	X-RAY DIFFRACTION	11	A	A	280 - 298	280 - 298
12	X-RAY DIFFRACTION	12	A	A	299 - 337	299 - 337
13	X-RAY DIFFRACTION	13	A	A	338 - 397	338 - 397
14	X-RAY DIFFRACTION	14	A	A	398 - 442	398 - 442
15	X-RAY DIFFRACTION	15	A	A	443 - 468	443 - 468
16	X-RAY DIFFRACTION	16	B	B	2 - 23	2 - 23
17	X-RAY DIFFRACTION	17	B	B	24 - 84	24 - 84
18	X-RAY DIFFRACTION	18	B	B	85 - 103	85 - 103
19	X-RAY DIFFRACTION	19	B	B	104 - 137	104 - 137
20	X-RAY DIFFRACTION	20	B	B	138 - 156	138 - 156
21	X-RAY DIFFRACTION	21	B	B	157 - 192	157 - 192
22	X-RAY DIFFRACTION	22	B	B	193 - 224	193 - 224
23	X-RAY DIFFRACTION	23	B	B	225 - 252	225 - 252
24	X-RAY DIFFRACTION	24	B	B	253 - 285	253 - 285
25	X-RAY DIFFRACTION	25	B	B	286 - 300	286 - 300
26	X-RAY DIFFRACTION	26	B	B	301 - 331	301 - 331
27	X-RAY DIFFRACTION	27	B	B	332 - 390	332 - 390
28	X-RAY DIFFRACTION	28	B	B	391 - 441	391 - 441
29	X-RAY DIFFRACTION	29	B	B	442 - 460	442 - 460
30	X-RAY DIFFRACTION	30	B	B	461 - 468	461 - 468

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