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- PDB-7ahl: ALPHA-HEMOLYSIN FROM STAPHYLOCOCCUS AUREUS -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7ahl
TitleALPHA-HEMOLYSIN FROM STAPHYLOCOCCUS AUREUS
ComponentsALPHA-HEMOLYSIN
KeywordsCYTOLYTIC PROTEIN / HEMOLYSIN / TRANSMEMBRANE PORE
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.89 Å
AuthorsSong, L. / Hobaugh, M. / Shustak, C. / Cheley, S. / Bayley, H. / Gouaux, J.E.
CitationJournal: Science / Year: 1996
Title: Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore.
Authors: Song, L. / Hobaugh, M.R. / Shustak, C. / Cheley, S. / Bayley, H. / Gouaux, J.E.
History
DepositionDec 2, 1996Processing site: BNL
Revision 1.0Jan 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-HEMOLYSIN
B: ALPHA-HEMOLYSIN
C: ALPHA-HEMOLYSIN
D: ALPHA-HEMOLYSIN
E: ALPHA-HEMOLYSIN
F: ALPHA-HEMOLYSIN
G: ALPHA-HEMOLYSIN


Theoretical massNumber of molelcules
Total (without water)233,0307
Polymers233,0307
Non-polymers00
Water14,736818
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41760 Å2
ΔGint-103 kcal/mol
Surface area77110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.920, 136.760, 135.120
Angle α, β, γ (deg.)90.00, 91.40, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.811688, -0.551879, 0.191292), (0.553101, 0.620971, -0.555404), (0.187729, 0.556619, 0.80928)19.62856, 8.32588, -19.24739
2given(0.370456, -0.699489, 0.611128), (0.690282, -0.232913, -0.685027), (0.621508, 0.675623, 0.396561)28.3028, 35.04865, -27.23743
3given(0.024331, -0.312771, 0.949517), (0.303417, -0.902685, -0.305119), (0.952547, 0.295524, 0.072937)18.74453, 60.15796, -17.69782
4given(0.025512, 0.312117, 0.949701), (-0.306431, -0.901836, 0.304618), (0.951551, -0.29879, 0.072635)-1.96817, 64.90733, 1.58792
5given(0.369966, 0.694372, 0.61723), (-0.702495, -0.22568, 0.674958), (0.607968, -0.683313, 0.404299)-17.32038, 46.65657, 17.44141
6given(0.803522, 0.561641, 0.197263), (-0.566043, 0.618319, 0.545231), (0.184252, -0.549764, 0.814745)-16.74873, 17.72835, 16.68814

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Components

#1: Protein
ALPHA-HEMOLYSIN / ALPHATOXIN


Mass: 33290.000 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Strain: WOOD46 / References: UniProt: P09616
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 60 %
Crystal growpH: 6
Details: PROTEIN WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES OF A PROTEIN SOLUTION OF 8 MG/ML PROTEIN, 25 MM BETA-OG, 10 MM TRIS AT PH 8.5 AND A PRECIPITANT SOLUTION OF 2.5 M (NH4)2SO4, 0.25% PEG 5K ...Details: PROTEIN WAS CRYSTALLIZED BY MIXING EQUAL VOLUMES OF A PROTEIN SOLUTION OF 8 MG/ML PROTEIN, 25 MM BETA-OG, 10 MM TRIS AT PH 8.5 AND A PRECIPITANT SOLUTION OF 2.5 M (NH4)2SO4, 0.25% PEG 5K MONOMETHYL ETHER AND 75MM SODIUM CACODYLATE, PH 6.0.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDCommon nameCrystal-IDSol-ID
1n-octyl-beta-glucoside11
2ammonium sulfate11
3mPEG500011

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→15 Å / Num. obs: 206863 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 8.7
Reflection shellResolution: 1.89→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.083 / Mean I/σ(I) obs: 3 / Rsym value: 0.349 / % possible all: 94.4
Reflection
*PLUS
Num. measured all: 2924665
Reflection shell
*PLUS
% possible obs: 94.4 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
bioteXdata reduction
bioteXdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.89→8 Å / σ(F): 2
Rfactor% reflectionSelection details
Rfree0.257 10 %RANDOM
Rwork0.199 --
obs0.199 93.3 %-
Refinement stepCycle: LAST / Resolution: 1.89→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16389 0 0 818 17207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 198341
Solvent computation
*PLUS
Displacement parameters
*PLUS

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