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- PDB-6h2d: Structure of the soluble AhlC of the tripartite alpha-pore formin... -

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Basic information

Entry
Database: PDB / ID: 6h2d
TitleStructure of the soluble AhlC of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
ComponentsAhlC
KeywordsTOXIN / Tripartite pore-forming toxin
Function / homologyHemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / membrane => GO:0016020 / Up-down Bundle / Mainly Alpha / membrane / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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

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Assembly

Deposited unit
P: AhlC
Q: AhlC
R: AhlC
S: AhlC


Theoretical massNumber of molelcules
Total (without water)117,7284
Polymers117,7284
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-10 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.070, 61.660, 129.770
Angle α, β, γ (deg.)90.00, 92.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AhlC


Mass: 29432.096 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: SAMN05880569_102658 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1N6TH80, UniProt: A0KLE2*PLUS

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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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Sodium chloride 0.1 M Tris pH 8 20 % (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2014
RadiationMonochromator: Double Crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.888
11-h,-k,l20.112
ReflectionResolution: 2.62→46.74 Å / Num. obs: 31150 / % possible obs: 99.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 37.858 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.058 / Net I/σ(I): 11
Reflection shellResolution: 2.62→2.69 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2309 / Rpim(I) all: 0.509 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet AhlC

Resolution: 2.62→46.74 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.86 / SU B: 15.437 / SU ML: 0.326 / Cross valid method: THROUGHOUT / ESU R: 0.789 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.33432 1448 4.7 %RANDOM
Rwork0.26909 ---
obs0.27218 29691 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.841 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å2-0.06 Å2
2--1.55 Å20 Å2
3----3.11 Å2
Refinement stepCycle: 1 / Resolution: 2.62→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6152 0 0 0 6152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0146178
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175679
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.6438361
X-RAY DIFFRACTIONr_angle_other_deg0.9551.62413306
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055798
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97725.623329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.468151114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.641529
X-RAY DIFFRACTIONr_chiral_restr0.0680.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02953
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_it4.9345.5463237
X-RAY DIFFRACTIONr_mcbond_other4.9345.5473236
X-RAY DIFFRACTIONr_mcangle_it7.1798.3024020
X-RAY DIFFRACTIONr_mcangle_other7.1788.3014021
X-RAY DIFFRACTIONr_scbond_it19.5786.12941
X-RAY DIFFRACTIONr_scbond_other19.5756.0992942
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other16.2188.9074342
X-RAY DIFFRACTIONr_long_range_B_refined13.77669.027096
X-RAY DIFFRACTIONr_long_range_B_other13.77669.0197097
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.62→2.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 97 -
Rwork0.341 2204 -
obs--99.96 %

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