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- PDB-6r1j: Structure of the soluble AhlC triple head mutant of the tripartit... -

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Basic information

Entry
Database: PDB / ID: 6r1j
TitleStructure of the soluble AhlC triple head mutant of the tripartite alpha-pore forming toxin, AHL, from Aeromonas hydrophila.
ComponentsUncharacterized protein
KeywordsTOXIN / Tripartite pore-forming toxin
Function / homologyHemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Up-down Bundle / Mainly Alpha / membrane / : / Uncharacterized protein
Function and homology information
Biological speciesAeromonas hydrophila J-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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
DepositionMar 14, 2019Deposition 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 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3534
Polymers58,3072
Non-polymers462
Water3,855214
1
J: Uncharacterized protein
D: Uncharacterized protein
hetero molecules

J: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7078
Polymers116,6154
Non-polymers924
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
Buried area11390 Å2
ΔGint-73 kcal/mol
Surface area45280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.538, 88.538, 290.975
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Uncharacterized protein


Mass: 29153.662 Da / Num. of mol.: 2 / Mutation: L156T, L160T, L161T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila J-1 (bacteria) / Gene: V469_08880 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1U6XZ15, UniProt: A0KLE2*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M imidazole pH 8.0, 10% PEG 8000

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.9→76.86 Å / Num. obs: 52765 / % possible obs: 100 % / Redundancy: 18.7 % / CC1/2: 0.997 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.9 Å / Num. unique obs: 2550

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H2E

6h2e


Resolution: 1.92→76.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.539 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27796 2550 4.8 %RANDOM
Rwork0.23449 ---
obs0.23658 50089 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.37 Å20 Å2
2--0.75 Å20 Å2
3----2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.92→76.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 2 214 4097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133926
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173676
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6315329
X-RAY DIFFRACTIONr_angle_other_deg1.4271.5628558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2835513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54425.419203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00515686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0591517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
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_it4.3114.8782058
X-RAY DIFFRACTIONr_mcbond_other4.314.8752057
X-RAY DIFFRACTIONr_mcangle_it5.8197.2762563
X-RAY DIFFRACTIONr_mcangle_other5.8187.2792564
X-RAY DIFFRACTIONr_scbond_it4.7845.3981868
X-RAY DIFFRACTIONr_scbond_other4.7835.4011869
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7767.9232765
X-RAY DIFFRACTIONr_long_range_B_refined8.40960.4834493
X-RAY DIFFRACTIONr_long_range_B_other8.42360.3644459
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 192 -
Rwork0.386 3622 -
obs--100 %

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