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- PDB-3c0m: Crystal structure of the proaerolysin mutant Y221G -

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Basic information

Entry
Database: PDB / ID: 3c0m
TitleCrystal structure of the proaerolysin mutant Y221G
ComponentsAerolysin
KeywordsTOXIN / CYTOLYTIC TOXIN / PORE-FORMING TOXIN / Membrane / Secreted
Function / homology
Function and homology information


symbiont-mediated cytolysis of host cell / toxin activity / host cell plasma membrane / extracellular region / identical protein binding / membrane
Similarity search - Function
Proaerolysin; Chain A, domain 2 / Proaerolysin, chain A, domain 2 / Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Proaerolysin, chain A, domain 3 / Aerolysin / : / Aerolysin toxin / Aerolysin toxin / Proaerolysin; Chain A, domain 3 ...Proaerolysin; Chain A, domain 2 / Proaerolysin, chain A, domain 2 / Pertussis Toxin; Chain B, domain 1 / Aerolysin/Pertussis toxin (APT), N-terminal domain / Proaerolysin, chain A, domain 3 / Aerolysin / : / Aerolysin toxin / Aerolysin toxin / Proaerolysin; Chain A, domain 3 / Aerolysin/Pertussis toxin domain / Aerolysin/Pertussis toxin (APT), N-terminal domain superfamily / Aerolysin/Pertussis toxin (APT) domain / Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / C-type lectin fold / Beta Complex / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsPernot, L. / Schiltz, M. / Thurnheer, S. / Burr, S.E. / van der Goot, G.
Citation
Journal: Nat.Chem.Biol. / Year: 2013
Title: Molecular assembly of the aerolysin pore reveals a swirling membrane-insertion mechanism.
Authors: Degiacomi, M.T. / Iacovache, I. / Pernot, L. / Chami, M. / Kudryashev, M. / Stahlberg, H. / van der Goot, F.G. / Dal Peraro, M.
#1: Journal: Nature / Year: 1994
Title: Structure of the Aeromonas toxin proaerolysin in its water-soluble and membrane-channel states.
Authors: Parker, M.W. / Buckley, J.T. / Postma, J.P. / Tucker, A.D. / Leonard, K. / Pattus, F. / Tsernoglou, D.
#2: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization of a proform of aerolysin, a hole-forming toxin from Aeromonas hydrophila.
Authors: Tucker, A.D. / Parker, M.W. / Tsernoglou, D. / Buckley, J.T.
History
DepositionJan 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aerolysin
B: Aerolysin


Theoretical massNumber of molelcules
Total (without water)103,7492
Polymers103,7492
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.618, 92.434, 169.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aerolysin


Mass: 51874.332 Da / Num. of mol.: 2 / Mutation: Y221G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: aerA / Plasmid: pMMB66EH / Production host: Aeromonas salmonicida (bacteria) / Strain (production host): CD3 / References: UniProt: P09167
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 9-11% PEG 4000, 100mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.82 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 2.88→44.58 Å / Num. all: 24769 / Num. obs: 24769 / % possible obs: 91.7 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.123 / Rsym value: 0.087 / Net I/σ(I): 10.39
Reflection shellResolution: 2.88→3 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.24 / Num. unique all: 6253 / Rsym value: 0.363 / % possible all: 67.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
MOLREPphasing
CNS1.1refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PRE

1pre


Resolution: 2.88→44.56 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1700 -RANDOM
Rwork0.199 ---
obs0.235 24754 93.5 %-
Displacement parametersBiso mean: 36.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å20 Å2
2--5.98 Å20 Å2
3----5.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.88→44.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7030 0 0 24 7054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.08
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.88→3.06 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.347 --
Rwork0.292 --
obs-3562 88.4 %

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