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

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Basic information

Entry
Database: PDB / ID: 6grj
TitleStructure of the AhlB pore of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
ComponentsAhlB
KeywordsTOXIN / Tripartite pore-forming toxin
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
Hemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / : / Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Alpha-helical pore-forming toxin family protein / Alpha-helical pore-forming toxin family protein
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.94 Å
AuthorsChurchill-Angus, A.M. / Wilson, J.S. / Baker, P.J.
CitationJournal: 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
DepositionJun 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: 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 1.2Jul 17, 2019Group: 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
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: AhlB
J: AhlB
A: AhlB
B: AhlB
C: AhlB
D: AhlB
E: AhlB
F: AhlB
H: AhlB
I: AhlB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,47963
Polymers390,44710
Non-polymers3,03253
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53100 Å2
ΔGint-821 kcal/mol
Surface area127090 Å2
MethodPISA
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 number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21J
12G
22A
13G
23B
14G
24C
15G
25D
16G
26E
17G
27F
18G
28H
19G
29I
110J
210A
111J
211B
112J
212C
113J
213D
114J
214E
115J
215F
116J
216H
117J
217I
118A
218B
119A
219C
120A
220D
121A
221E
122A
222F
123A
223H
124A
224I
125B
225C
126B
226D
127B
227E
128B
228F
129B
229H
130B
230I
131C
231D
132C
232E
133C
233F
134C
234H
135C
235I
136D
236E
137D
237F
138D
238H
139D
239I
140E
240F
141E
241H
142E
242I
143F
243H
144F
244I
145H
245I

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNILEILEGA16 - 33616 - 336
21GLNGLNILEILEJB16 - 33616 - 336
12THRTHRPROPROGA2 - 3412 - 341
22THRTHRPROPROAC2 - 3412 - 341
13GLNGLNILEILEGA16 - 33616 - 336
23GLNGLNILEILEBD16 - 33616 - 336
14THRTHRPROPROGA2 - 3412 - 341
24THRTHRPROPROCE2 - 3412 - 341
15ASNASNILEILEGA15 - 33615 - 336
25ASNASNILEILEDF15 - 33615 - 336
16THRTHRPROPROGA2 - 3412 - 341
26THRTHRPROPROEG2 - 3412 - 341
17ALAALAILEILEGA17 - 33617 - 336
27ALAALAILEILEFH17 - 33617 - 336
18THRTHRPROPROGA2 - 3412 - 341
28THRTHRPROPROHI2 - 3412 - 341
19GLNGLNILEILEGA16 - 33616 - 336
29GLNGLNILEILEIJ16 - 33616 - 336
110GLNGLNILEILEJB16 - 33616 - 336
210GLNGLNILEILEAC16 - 33616 - 336
111GLNGLNALAALAJB16 - 33716 - 337
211GLNGLNALAALABD16 - 33716 - 337
112GLNGLNILEILEJB16 - 33616 - 336
212GLNGLNILEILECE16 - 33616 - 336
113GLNGLNALAALAJB16 - 33716 - 337
213GLNGLNALAALADF16 - 33716 - 337
114GLNGLNILEILEJB16 - 33616 - 336
214GLNGLNILEILEEG16 - 33616 - 336
115ALAALAALAALAJB17 - 33717 - 337
215ALAALAALAALAFH17 - 33717 - 337
116GLNGLNILEILEJB16 - 33616 - 336
216GLNGLNILEILEHI16 - 33616 - 336
117GLNGLNALAALAJB16 - 33716 - 337
217GLNGLNALAALAIJ16 - 33716 - 337
118GLNGLNILEILEAC16 - 33616 - 336
218GLNGLNILEILEBD16 - 33616 - 336
119THRTHRPROPROAC2 - 3412 - 341
219THRTHRPROPROCE2 - 3412 - 341
120ASNASNILEILEAC15 - 33615 - 336
220ASNASNILEILEDF15 - 33615 - 336
121THRTHRPROPROAC2 - 3412 - 341
221THRTHRPROPROEG2 - 3412 - 341
122ALAALAILEILEAC17 - 33617 - 336
222ALAALAILEILEFH17 - 33617 - 336
123THRTHRPROPROAC2 - 3412 - 341
223THRTHRPROPROHI2 - 3412 - 341
124GLNGLNILEILEAC16 - 33616 - 336
224GLNGLNILEILEIJ16 - 33616 - 336
125GLNGLNILEILEBD16 - 33616 - 336
225GLNGLNILEILECE16 - 33616 - 336
126GLNGLNALAALABD16 - 33716 - 337
226GLNGLNALAALADF16 - 33716 - 337
127GLNGLNILEILEBD16 - 33616 - 336
227GLNGLNILEILEEG16 - 33616 - 336
128ALAALAALAALABD17 - 33717 - 337
228ALAALAALAALAFH17 - 33717 - 337
129GLNGLNILEILEBD16 - 33616 - 336
229GLNGLNILEILEHI16 - 33616 - 336
130GLNGLNALAALABD16 - 33716 - 337
230GLNGLNALAALAIJ16 - 33716 - 337
131ASNASNILEILECE15 - 33615 - 336
231ASNASNILEILEDF15 - 33615 - 336
132THRTHRPROPROCE2 - 3412 - 341
232THRTHRPROPROEG2 - 3412 - 341
133ALAALAILEILECE17 - 33617 - 336
233ALAALAILEILEFH17 - 33617 - 336
134THRTHRPROPROCE2 - 3412 - 341
234THRTHRPROPROHI2 - 3412 - 341
135GLNGLNILEILECE16 - 33616 - 336
235GLNGLNILEILEIJ16 - 33616 - 336
136ASNASNILEILEDF15 - 33615 - 336
236ASNASNILEILEEG15 - 33615 - 336
137ALAALAILEILEDF17 - 33617 - 336
237ALAALAILEILEFH17 - 33617 - 336
138ASNASNILEILEDF15 - 33615 - 336
238ASNASNILEILEHI15 - 33615 - 336
139GLNGLNALAALADF16 - 33716 - 337
239GLNGLNALAALAIJ16 - 33716 - 337
140ALAALAILEILEEG17 - 33617 - 336
240ALAALAILEILEFH17 - 33617 - 336
141THRTHRPROPROEG2 - 3412 - 341
241THRTHRPROPROHI2 - 3412 - 341
142GLNGLNILEILEEG16 - 33616 - 336
242GLNGLNILEILEIJ16 - 33616 - 336
143ALAALAILEILEFH17 - 33617 - 336
243ALAALAILEILEHI17 - 33617 - 336
144ALAALAALAALAFH17 - 33717 - 337
244ALAALAALAALAIJ17 - 33717 - 337
145GLNGLNILEILEHI16 - 33616 - 336
245GLNGLNILEILEIJ16 - 33616 - 336

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45

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Components

#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


Mass: 118.174 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-CL / CHLORIDE ION


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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.25 Å3/Da / Density % sol: 76.58 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97938 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.94→107.58 Å / Num. obs: 169188 / % possible obs: 99 % / Redundancy: 3.5 % / Net I/σ(I): 1.127
Reflection shellResolution: 2.94→2.99 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
DIALSdata reduction
DIALSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.94→102.67 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc 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
RfactorNum. reflection% reflectionSelection details
Rfree0.23865 8353 4.9 %RANDOM
Rwork0.22238 ---
obs0.22319 160701 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 67.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å22.23 Å2
2---0.59 Å20 Å2
3----2.65 Å2
Refinement stepCycle: 1 / Resolution: 2.94→102.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24221 0 159 0 24380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01424590
X-RAY DIFFRACTIONr_bond_other_d0.0010.01722812
X-RAY DIFFRACTIONr_angle_refined_deg1.571.65433520
X-RAY DIFFRACTIONr_angle_other_deg1.0371.67253158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4953269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80726.1741069
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.327153916
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.621560
X-RAY DIFFRACTIONr_chiral_restr0.0830.23590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227804
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024008
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.896.79213124
X-RAY DIFFRACTIONr_mcbond_other5.896.79213123
X-RAY DIFFRACTIONr_mcangle_it8.77110.19116374
X-RAY DIFFRACTIONr_mcangle_other8.77110.19116375
X-RAY DIFFRACTIONr_scbond_it6.7937.15911466
X-RAY DIFFRACTIONr_scbond_other6.7767.15411459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.08410.57317134
X-RAY DIFFRACTIONr_long_range_B_refined12.0685.71129275
X-RAY DIFFRACTIONr_long_range_B_other12.0685.71229276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11G91800.14
12J91800.14
21G110670.05
22A110670.05
31G91960.14
32B91960.14
41G110700.05
42C110700.05
51G91750.14
52D91750.14
61G110890.04
62E110890.04
71G90810.14
72F90810.14
81G110430.05
82H110430.05
91G90540.13
92I90540.13
101J91650.14
102A91650.14
111J106830.06
112B106830.06
121J91420.14
122C91420.14
131J106080.05
132D106080.05
141J91540.14
142E91540.14
151J104870.06
152F104870.06
161J91380.13
162H91380.13
171J104420.04
172I104420.04
181A92010.13
182B92010.13
191A111030.05
192C111030.05
201A91630.14
202D91630.14
211A110980.04
212E110980.04
221A90710.14
222F90710.14
231A109920.05
232H109920.05
241A90400.13
242I90400.13
251B91780.14
252C91780.14
261B106410.05
262D106410.05
271B91800.13
272E91800.13
281B104780.07
282F104780.07
291B91530.14
292H91530.14
301B104390.06
302I104390.06
311C91450.14
312D91450.14
321C110630.05
322E110630.05
331C90470.14
332F90470.14
341C110060.04
342H110060.04
351C90250.14
352I90250.14
361D91550.14
362E91550.14
371D104130.07
372F104130.07
381D91650.14
382H91650.14
391D104880.05
392I104880.05
401E90820.14
402F90820.14
411E110660.04
412H110660.04
421E90520.13
422I90520.13
431F90560.14
432H90560.14
441F104500.05
442I104500.05
451H90460.14
452I90460.14
LS refinement shellResolution: 2.939→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 567 -
Rwork0.357 11726 -
obs--97.84 %

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