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- PDB-6h2f: Structure of the pre-pore AhlB of the tripartite alpha-pore formi... -

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Basic information

Entry
Database: PDB / ID: 6h2f
TitleStructure of the pre-pore AhlB of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
ComponentsAhlB
KeywordsTOXIN / Tripartite pore-forming toxin
Function / homologyHemolysin BL-binding component / Bacillus haemolytic enterotoxin (HBL) / membrane => GO:0016020 / PHOSPHATE ION / Alpha-helical pore-forming toxin family protein / Uncharacterized protein
Function and homology information
Biological speciesAeromonas hydrophila AL09-71 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChurchill-Angus, A.M. / Wilson, J.S. / Baker, P.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/F016832/1 United Kingdom
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
DepositionJul 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)387,72514
Polymers387,34510
Non-polymers3804
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy, Pore-like structures observed by electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48320 Å2
ΔGint-307 kcal/mol
Surface area128680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.661, 178.184, 485.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
AhlB


Mass: 38734.520 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila AL09-71 (bacteria)
Gene: A9R12_16795 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A081US78, UniProt: A0KLE1*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4

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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: 3.29 Å3/Da / Density % sol: 62.61 % / Description: Stacked plates
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium phosphate 0.1 M Tris pH 8.5 50 % (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2014
RadiationMonochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.55→39.55 Å / Num. obs: 165574 / % possible obs: 100 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.188 / Rpim(I) all: 0.122 / Net I/σ(I): 6.6
Reflection shellResolution: 2.55→2.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 29762 / Rrim(I) all: 0.751 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
Aimless0.3.6data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet AhlB

Resolution: 2.55→39.55 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.054 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.324 / ESU R Free: 0.287 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27844 8380 5.1 %RANDOM
Rwork0.19052 ---
obs0.19497 156934 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å20 Å2
2--1.53 Å20 Å2
3----3.13 Å2
Refinement stepCycle: 1 / Resolution: 2.55→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24746 0 20 0 24766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01425028
X-RAY DIFFRACTIONr_bond_other_d0.0010.01723132
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.63734111
X-RAY DIFFRACTIONr_angle_other_deg0.9831.63853946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18253345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41926.071089
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.195154150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0331564
X-RAY DIFFRACTIONr_chiral_restr0.0750.23626
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0228430
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024094
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_it87.013.58613425
X-RAY DIFFRACTIONr_mcbond_other87.0133.58513424
X-RAY DIFFRACTIONr_mcangle_it69.25.52616755
X-RAY DIFFRACTIONr_mcangle_other69.1995.52616756
X-RAY DIFFRACTIONr_scbond_it71.5454.14811603
X-RAY DIFFRACTIONr_scbond_other70.6854.14111588
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other61.635.75617333
X-RAY DIFFRACTIONr_long_range_B_refined72.76445.28129028
X-RAY DIFFRACTIONr_long_range_B_other72.76345.28329029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 611 -
Rwork0.27 11466 -
obs--99.85 %

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