PDB-6grj: Structure of the AhlB pore of the tripartite alpha-pore forming t...

ID or keywords:

Entry

Database: PDB / ID: 6grj

Title

Structure of the AhlB pore of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.

Components

AhlB

Keywords

TOXIN / Tripartite pore-forming toxin

Function / homology

Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / membrane => GO:0016020 /

membrane /

PHOSPHATE ION / Alpha-helical pore-forming toxin family protein / Alpha-helical pore-forming toxin family protein

Function and homology information

Biological species

Aeromonas hydrophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.94 Å

Authors

Churchill-Angus, A.M. / Wilson, J.S. / Baker, P.J.

Citation

Journal: Nat Commun / Year: 2019
Title: Identification and structural analysis of the tripartite alpha-pore forming toxin of Aeromonas hydrophila.
Authors: Wilson, J.S. / Churchill-Angus, A.M. / Davies, S.P. / Sedelnikova, S.E. / Tzokov, S.B. / Rafferty, J.B. / Bullough, P.A. / Bisson, C. / Baker, P.J.

History

Deposition	Jun 11, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 3, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jul 10, 2019	Group: Data collection / Database references Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_seq_map_depositor_info Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code
Revision 1.2	Jul 17, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6grj.cif.gz	594.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/6grj ftp://data.pdbj.org/pub/pdb/validation_reports/gr/6grj	HTTPS FTP

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Related structure data

Related structure data	6grkC 6h2dC 6h2eC 6h2fC 6r1jC C: citing same article (ref.)
Similar structure data	6h2f-d 7a0g-d 2502 6zca-d 21025 21921 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

G: AhlB

J: AhlB

A: AhlB

B: AhlB

C: AhlB

D: AhlB

E: AhlB

F: AhlB

H: AhlB

I: AhlB

hetero molecules

393 kDa, 10 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)	363.644, 116.526, 217.409
Angle α, β, γ (deg.)	90.00, 118.01, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	G	16 - 336
2	1	J	16 - 336
1	2	G	2 - 341
2	2	A	2 - 341
1	3	G	16 - 336
2	3	B	16 - 336
1	4	G	2 - 341
2	4	C	2 - 341
1	5	G	15 - 336
2	5	D	15 - 336
1	6	G	2 - 341
2	6	E	2 - 341
1	7	G	17 - 336
2	7	F	17 - 336
1	8	G	2 - 341
2	8	H	2 - 341
1	9	G	16 - 336
2	9	I	16 - 336
1	10	J	16 - 336
2	10	A	16 - 336
1	11	J	16 - 337
2	11	B	16 - 337
1	12	J	16 - 336
2	12	C	16 - 336
1	13	J	16 - 337
2	13	D	16 - 337
1	14	J	16 - 336
2	14	E	16 - 336
1	15	J	17 - 337
2	15	F	17 - 337
1	16	J	16 - 336
2	16	H	16 - 336
1	17	J	16 - 337
2	17	I	16 - 337
1	18	A	16 - 336
2	18	B	16 - 336
1	19	A	2 - 341
2	19	C	2 - 341
1	20	A	15 - 336
2	20	D	15 - 336
1	21	A	2 - 341
2	21	E	2 - 341
1	22	A	17 - 336
2	22	F	17 - 336
1	23	A	2 - 341
2	23	H	2 - 341
1	24	A	16 - 336
2	24	I	16 - 336
1	25	B	16 - 336
2	25	C	16 - 336
1	26	B	16 - 337
2	26	D	16 - 337
1	27	B	16 - 336
2	27	E	16 - 336
1	28	B	17 - 337
2	28	F	17 - 337
1	29	B	16 - 336
2	29	H	16 - 336
1	30	B	16 - 337
2	30	I	16 - 337
1	31	C	15 - 336
2	31	D	15 - 336
1	32	C	2 - 341
2	32	E	2 - 341
1	33	C	17 - 336
2	33	F	17 - 336
1	34	C	2 - 341
2	34	H	2 - 341
1	35	C	16 - 336
2	35	I	16 - 336
1	36	D	15 - 336
2	36	E	15 - 336
1	37	D	17 - 336
2	37	F	17 - 336
1	38	D	15 - 336
2	38	H	15 - 336
1	39	D	16 - 337
2	39	I	16 - 337
1	40	E	17 - 336
2	40	F	17 - 336
1	41	E	2 - 341
2	41	H	2 - 341
1	42	E	16 - 336
2	42	I	16 - 336
1	43	F	17 - 336
2	43	H	17 - 336
1	44	F	17 - 337
2	44	I	17 - 337
1	45	H	16 - 336
2	45	I	16 - 336

NCS ensembles :

#1: Protein	AhlB Mass: 39044.742 Da / Num. of mol.: 10 / Mutation: M336I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: A9R12_16795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A081US78, UniProt: A0A454GEH4*PLUS
#2: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Chemical	... ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 5.25 Å³/Da / Density % sol: 76.58 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 60% Methyl-2,4-Pentanediol (MPD), 0.2M Ammonium phosphate, 0.1M Tris pH8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97938 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97938 Å / Relative weight: 1
Reflection	Resolution: 2.94→107.58 Å / Num. obs: 169188 / % possible obs: 99 % / Redundancy: 3.5 % / Net I/σ(I): 1.127
Reflection shell	Resolution: 2.94→2.99 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
DIALS		data reduction
DIALS		data scaling
SHELXDE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.94→102.67 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.923 / SU B: 14.884 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.415 / ESU R Free: 0.279 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23865	8353	4.9 %	RANDOM
R_work	0.22238	-	-	-
obs	0.22319	160701	98.93 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 67.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.37 Å²	0 Å²	2.23 Å²
2-	-	-0.59 Å²	0 Å²
3-	-	-	-2.65 Å²

Refinement step

Cycle: 1 / Resolution: 2.94→102.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24221	0	159	0	24380

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.014	24590
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	22812
X-RAY DIFFRACTION	r_angle_refined_deg	1.57	1.654	33520
X-RAY DIFFRACTION	r_angle_other_deg	1.037	1.672	53158
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.49	5	3269
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.807	26.174	1069
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.327	15	3916
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.62	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	3590
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	27804
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4008
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	5.89	6.792	13124
X-RAY DIFFRACTION	r_mcbond_other	5.89	6.792	13123
X-RAY DIFFRACTION	r_mcangle_it	8.771	10.191	16374
X-RAY DIFFRACTION	r_mcangle_other	8.771	10.191	16375
X-RAY DIFFRACTION	r_scbond_it	6.793	7.159	11466
X-RAY DIFFRACTION	r_scbond_other	6.776	7.154	11459
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	10.084	10.573	17134
X-RAY DIFFRACTION	r_long_range_B_refined	12.06	85.711	29275
X-RAY DIFFRACTION	r_long_range_B_other	12.06	85.712	29276
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	G	9180	0.14
1	2	J	9180	0.14
2	1	G	11067	0.05
2	2	A	11067	0.05
3	1	G	9196	0.14
3	2	B	9196	0.14
4	1	G	11070	0.05
4	2	C	11070	0.05
5	1	G	9175	0.14
5	2	D	9175	0.14
6	1	G	11089	0.04
6	2	E	11089	0.04
7	1	G	9081	0.14
7	2	F	9081	0.14
8	1	G	11043	0.05
8	2	H	11043	0.05
9	1	G	9054	0.13
9	2	I	9054	0.13
10	1	J	9165	0.14
10	2	A	9165	0.14
11	1	J	10683	0.06
11	2	B	10683	0.06
12	1	J	9142	0.14
12	2	C	9142	0.14
13	1	J	10608	0.05
13	2	D	10608	0.05
14	1	J	9154	0.14
14	2	E	9154	0.14
15	1	J	10487	0.06
15	2	F	10487	0.06
16	1	J	9138	0.13
16	2	H	9138	0.13
17	1	J	10442	0.04
17	2	I	10442	0.04
18	1	A	9201	0.13
18	2	B	9201	0.13
19	1	A	11103	0.05
19	2	C	11103	0.05
20	1	A	9163	0.14
20	2	D	9163	0.14
21	1	A	11098	0.04
21	2	E	11098	0.04
22	1	A	9071	0.14
22	2	F	9071	0.14
23	1	A	10992	0.05
23	2	H	10992	0.05
24	1	A	9040	0.13
24	2	I	9040	0.13
25	1	B	9178	0.14
25	2	C	9178	0.14
26	1	B	10641	0.05
26	2	D	10641	0.05
27	1	B	9180	0.13
27	2	E	9180	0.13
28	1	B	10478	0.07
28	2	F	10478	0.07
29	1	B	9153	0.14
29	2	H	9153	0.14
30	1	B	10439	0.06
30	2	I	10439	0.06
31	1	C	9145	0.14
31	2	D	9145	0.14
32	1	C	11063	0.05
32	2	E	11063	0.05
33	1	C	9047	0.14
33	2	F	9047	0.14
34	1	C	11006	0.04
34	2	H	11006	0.04
35	1	C	9025	0.14
35	2	I	9025	0.14
36	1	D	9155	0.14
36	2	E	9155	0.14
37	1	D	10413	0.07
37	2	F	10413	0.07
38	1	D	9165	0.14
38	2	H	9165	0.14
39	1	D	10488	0.05
39	2	I	10488	0.05
40	1	E	9082	0.14
40	2	F	9082	0.14
41	1	E	11066	0.04
41	2	H	11066	0.04
42	1	E	9052	0.13
42	2	I	9052	0.13
43	1	F	9056	0.14
43	2	H	9056	0.14
44	1	F	10450	0.05
44	2	I	10450	0.05
45	1	H	9046	0.14
45	2	I	9046	0.14

LS refinement shell

Resolution: 2.939→3.016 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	567	-
R_work	0.357	11726	-
obs	-	-	97.84 %

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