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- PDB-6grk: Structure of the soluble AhlB of the tripartite alpha-pore formin... -

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Basic information

Entry
Database: PDB / ID: 6grk
TitleStructure of the soluble 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 / membrane / Alpha-helical pore-forming toxin family protein / Alpha-helical pore-forming toxin family protein
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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
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
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 1.3May 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
A: AhlB
I: AhlB
B: AhlB


Theoretical massNumber of molelcules
Total (without water)116,2043
Polymers116,2043
Non-polymers00
Water1,820101
1
A: AhlB


Theoretical massNumber of molelcules
Total (without water)38,7351
Polymers38,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: AhlB


Theoretical massNumber of molelcules
Total (without water)38,7351
Polymers38,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: AhlB


Theoretical massNumber of molelcules
Total (without water)38,7351
Polymers38,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.470, 79.810, 111.010
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11I-410-

HOH

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Components

#1: Protein AhlB


Mass: 38734.520 Da / Num. of mol.: 3
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M potassium thiocyanate, 0.1 M bis-tris propane pH 6.5, and 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.895
11-1/2H+3/2K, -1/2H-1/2K, L20.105
ReflectionResolution: 2.33→58.34 Å / Num. obs: 49043 / % possible obs: 98.1 % / Redundancy: 3.3 % / Net I/σ(I): 0.791
Reflection shellResolution: 2.33→2.39 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→58.41 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.863 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25361 2504 5.1 %RANDOM
Rwork0.22232 ---
obs0.22391 46538 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.943 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å21.64 Å2
2--1.26 Å20 Å2
3---0.3 Å2
Refinement stepCycle: 1 / Resolution: 2.33→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7774 0 0 101 7875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0147860
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177271
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.63610714
X-RAY DIFFRACTIONr_angle_other_deg0.9671.63716957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.59251051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94625.988344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.384151301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0871521
X-RAY DIFFRACTIONr_chiral_restr0.0720.21138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028940
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021288
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_it3.7084.8614216
X-RAY DIFFRACTIONr_mcbond_other3.7054.864215
X-RAY DIFFRACTIONr_mcangle_it5.4967.2825263
X-RAY DIFFRACTIONr_mcangle_other5.4967.2835264
X-RAY DIFFRACTIONr_scbond_it3.7135.1013644
X-RAY DIFFRACTIONr_scbond_other3.7125.1023645
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6527.5355452
X-RAY DIFFRACTIONr_long_range_B_refined7.70559.8929175
X-RAY DIFFRACTIONr_long_range_B_other7.70459.9039169
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.33→2.391 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 195 -
Rwork0.309 3462 -
obs--99.75 %

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