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- PDB-1pre: PROAEROLYSIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1pre
TitlePROAEROLYSIN
ComponentsPROAEROLYSIN
KeywordsTOXIN (HEMOLYTIC POLYPEPTIDE)
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 / Resolution: 2.8 Å
AuthorsParker, M.W. / Buckley, J.T. / Postma, J.P.M. / Tucker, A.D. / Tsernoglou, D.
Citation
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.
#1: Journal: To be Published
Title: Structural Analysis of Proaerolysin and Various Single-Site Mutants as a Basis for Understanding Membrane Insertion of the Toxin
Authors: Parker, M.W. / Buckley, J.T. / Postma, J.P.M. / Feil, S.C. / Van Der Goot, F.G. / Vetter, I. / Tucker, A.D. / 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
DepositionSep 15, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROAEROLYSIN
B: PROAEROLYSIN


Theoretical massNumber of molelcules
Total (without water)103,9612
Polymers103,9612
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-3 kcal/mol
Surface area39860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.000, 104.000, 222.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.00043, 0.00286), (-0.00281, 0.37045, -0.92885), (-0.00066, -0.92885, -0.37045)
Vector: 31.53877, 64.08936, 93.57151)

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Components

#1: Protein PROAEROLYSIN


Mass: 51980.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Plasmid: PRK2013 / Production host: Aeromonas salmonicida (bacteria) / References: UniProt: P09167
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57 %
Crystal growpH: 5.6 / Details: pH 5.6
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Tucker, A.D., (1990) J.Mol.Biol., 212, 561. / pH: 5.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.0 mg/mlprotein1drop
2100 mMacetate1reservoirpH5.4
31-2 %PEG40001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 30060 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.091
Reflection
*PLUS
Num. measured all: 145443

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Processing

Software
NameClassification
MOSFLMdata reduction
PROLSQrefinement
RefinementResolution: 2.8→6 Å / σ(F): 0 /
Num. reflection% reflection
obs26993 98 %
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 2.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7056 0 0 33 7089
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0440.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.045
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.751
X-RAY DIFFRACTIONp_mcangle_it1.421.5
X-RAY DIFFRACTIONp_scbond_it0.661
X-RAY DIFFRACTIONp_scangle_it1.21.5
X-RAY DIFFRACTIONp_plane_restr0.0090.02
X-RAY DIFFRACTIONp_chiral_restr0.1480.15
X-RAY DIFFRACTIONp_singtor_nbd0.2290.5
X-RAY DIFFRACTIONp_multtor_nbd0.3050.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2220.5
X-RAY DIFFRACTIONp_planar_tor1.63
X-RAY DIFFRACTIONp_staggered_tor21.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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