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- PDB-4yhd: Staphylococcal alpha-hemolysin H35A mutant monomer -

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Basic information

Entry
Database: PDB / ID: 4yhd
TitleStaphylococcal alpha-hemolysin H35A mutant monomer
ComponentsAlpha-hemolysin
KeywordsTOXIN / monomer / immunoglobulin like fold
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 / SYNCHROTRON / Resolution: 2.801 Å
AuthorsSugawara, T. / Kato, K. / Tanaka, Y. / Yao, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS26102501 Japan
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
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Mar 21, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
G: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,81311
Polymers206,6366
Non-polymers1775
Water00
1
A: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4752
Polymers34,4391
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4752
Polymers34,4391
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-hemolysin


Theoretical massNumber of molelcules
Total (without water)34,4391
Polymers34,4391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4752
Polymers34,4391
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4752
Polymers34,4391
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
G: Alpha-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4752
Polymers34,4391
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.930, 128.910, 135.280
Angle α, β, γ (deg.)90.00, 91.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alpha-hemolysin / Alpha-HL / Alpha-toxin


Mass: 34439.293 Da / Num. of mol.: 6 / Fragment: UNP residues 27-319 / Mutation: H35A, D208E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hly, hla / Production host: Escherichia coli (E. coli) / References: UniProt: P09616
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: sodium cacodylate. calcium chloride, supermine, 2-propanol, ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.13 Å / Num. obs: 61440 / % possible obs: 95.8 % / Redundancy: 3.62 % / Net I/σ(I): 10

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 2.801→37.393 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 3070 5 %
Rwork0.215 --
obs0.2174 61414 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→37.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13499 0 5 0 13504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413796
X-RAY DIFFRACTIONf_angle_d0.77718666
X-RAY DIFFRACTIONf_dihedral_angle_d13.8655079
X-RAY DIFFRACTIONf_chiral_restr0.0312003
X-RAY DIFFRACTIONf_plane_restr0.0032390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.84460.37970.31621845X-RAY DIFFRACTION68
2.8446-2.89130.3421080.29332054X-RAY DIFFRACTION75
2.8913-2.94110.31991200.28642280X-RAY DIFFRACTION81
2.9411-2.99460.32461300.27622476X-RAY DIFFRACTION91
2.9946-3.05210.34421430.27612725X-RAY DIFFRACTION98
3.0521-3.11440.3461450.26942739X-RAY DIFFRACTION100
3.1144-3.18210.33661440.2592749X-RAY DIFFRACTION100
3.1821-3.25610.3031450.25552743X-RAY DIFFRACTION100
3.2561-3.33740.35351450.26612762X-RAY DIFFRACTION100
3.3374-3.42760.33671450.24762748X-RAY DIFFRACTION100
3.4276-3.52840.27291430.22682728X-RAY DIFFRACTION100
3.5284-3.64220.27971470.21682795X-RAY DIFFRACTION100
3.6422-3.77230.25061450.21822742X-RAY DIFFRACTION100
3.7723-3.92310.25911450.20682760X-RAY DIFFRACTION100
3.9231-4.10150.24871450.19222756X-RAY DIFFRACTION100
4.1015-4.31740.22941450.182758X-RAY DIFFRACTION100
4.3174-4.58750.17081460.16142772X-RAY DIFFRACTION100
4.5875-4.94090.19811450.15642767X-RAY DIFFRACTION100
4.9409-5.43680.21941460.17382782X-RAY DIFFRACTION100
5.4368-6.22040.24451470.19982781X-RAY DIFFRACTION100
6.2204-7.82520.25691450.20672771X-RAY DIFFRACTION100
7.8252-37.39680.24351490.22512811X-RAY DIFFRACTION99

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