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- PDB-4p24: pore forming toxin -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4p24
Titlepore forming toxin
ComponentsAlpha-hemolysin
KeywordsTOXIN / pore forming toxin
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / extracellular region
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
Alpha-hemolysin / Alpha-hemolysin
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsSugawara, T. / Yamashita, D. / Tanaka, Y. / Tanaka, I. / Yao, M.
CitationJournal: Toxicon / Year: 2015
Title: Structural basis for pore-forming mechanism of staphylococcal alpha-hemolysin.
Authors: Sugawara, T. / Yamashita, D. / Kato, K. / Peng, Z. / Ueda, J. / Kaneko, J. / Kamio, Y. / Tanaka, Y. / Yao, M.
History
DepositionMar 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords / symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text / _symmetry.Int_Tables_number
Revision 1.2Dec 27, 2023Group: 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 / refine_hist / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,67220
Polymers240,1367
Non-polymers1,53613
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45480 Å2
ΔGint-245 kcal/mol
Surface area76990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.060, 170.060, 202.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Alpha-hemolysin / Hla


Mass: 34305.117 Da / Num. of mol.: 7 / Mutation: W179A,R200A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / Gene: SAV1163 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99UU6, UniProt: A0A0J9X1Z2*PLUS
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM

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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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 40% MPD, 0.1M citric acid pH4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→48.6 Å / Num. obs: 54499 / % possible obs: 99.99 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.2054 / Net I/σ(I): 10.81
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.9913 / Mean I/σ(I) obs: 2.13 / % possible all: 99.98

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 3.1→48.6 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 2724 5 %
Rwork0.219 --
obs0.2202 54482 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16225 0 104 0 16329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416666
X-RAY DIFFRACTIONf_angle_d0.84322554
X-RAY DIFFRACTIONf_dihedral_angle_d13.8076121
X-RAY DIFFRACTIONf_chiral_restr0.0322429
X-RAY DIFFRACTIONf_plane_restr0.0032894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.15640.32031400.2812686X-RAY DIFFRACTION100
3.1564-3.21710.3131420.2722675X-RAY DIFFRACTION100
3.2171-3.28270.30441410.27292685X-RAY DIFFRACTION100
3.2827-3.35410.28471390.26032670X-RAY DIFFRACTION100
3.3541-3.43210.27751420.24192691X-RAY DIFFRACTION100
3.4321-3.51790.24821420.23792689X-RAY DIFFRACTION100
3.5179-3.6130.28231430.22162704X-RAY DIFFRACTION100
3.613-3.71920.28161410.21822668X-RAY DIFFRACTION100
3.7192-3.83920.2751430.22242722X-RAY DIFFRACTION100
3.8392-3.97640.22991410.21482683X-RAY DIFFRACTION100
3.9764-4.13550.23211430.20292730X-RAY DIFFRACTION100
4.1355-4.32360.20911430.18812705X-RAY DIFFRACTION100
4.3236-4.55140.21251430.18372711X-RAY DIFFRACTION100
4.5514-4.83640.19161440.16862738X-RAY DIFFRACTION100
4.8364-5.20940.20021430.18382731X-RAY DIFFRACTION100
5.2094-5.73290.2071440.20282750X-RAY DIFFRACTION100
5.7329-6.56070.28541470.25012774X-RAY DIFFRACTION100
6.5607-8.25920.22531480.23272803X-RAY DIFFRACTION100
8.2592-48.60590.25791550.24252943X-RAY DIFFRACTION100

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