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- PDB-6h2e: Structure of the soluble AhlC of the tripartite alpha-pore formin... -

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Basic information

Entry
Database: PDB / ID: 6h2e
TitleStructure of the soluble AhlC of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
ComponentsAhlC
KeywordsTOXIN / Tripartite pore-forming toxin
Function / homologymembrane / : / Uncharacterized protein
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)58,8642
Polymers58,8642
Non-polymers00
Water00
1
P: AhlC
Q: AhlC

P: AhlC
Q: AhlC


Theoretical massNumber of molelcules
Total (without water)117,7284
Polymers117,7284
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area11830 Å2
ΔGint-30 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.710, 134.710, 145.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein AhlC


Mass: 29432.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: V469_08880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U6XZ15, 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: 3.23 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2 M Magnesium chloride 0.1 M Tris pH 7 10 % (w/v) PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2015
RadiationMonochromator: Double crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.35→58.33 Å / Num. obs: 32942 / % possible obs: 99.8 % / Redundancy: 39.3 % / Biso Wilson estimate: 48.86 Å2 / Rpim(I) all: 0.023 / Net I/σ(I): 19.8
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 40.7 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 97395 / Rpim(I) all: 0.639 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→58.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27364 1589 4.8 %RANDOM
Rwork0.22655 ---
obs0.22874 31303 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.846 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2--1.69 Å20 Å2
3----3.37 Å2
Refinement stepCycle: 1 / Resolution: 2.35→58.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3866 0 0 0 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0143897
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173603
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.6425287
X-RAY DIFFRACTIONr_angle_other_deg1.5011.6258439
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5395508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.86225.5200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.73515685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.9751517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024419
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02613
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_it6.3236.52047
X-RAY DIFFRACTIONr_mcbond_other6.3166.52046
X-RAY DIFFRACTIONr_mcangle_it8.0439.7362550
X-RAY DIFFRACTIONr_mcangle_other8.0439.7372551
X-RAY DIFFRACTIONr_scbond_it7.7327.191850
X-RAY DIFFRACTIONr_scbond_other7.737.1891851
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.04110.5322738
X-RAY DIFFRACTIONr_long_range_B_refined11.17480.1044365
X-RAY DIFFRACTIONr_long_range_B_other11.17380.0974366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 110 -
Rwork0.218 2270 -
obs--99.66 %

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