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- PDB-3i41: Crystal structure of beta toxin from Staphylococcus aureus F277A,... -

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Basic information

Entry
Database: PDB / ID: 3i41
TitleCrystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant
ComponentsBeta-hemolysin
KeywordsTOXIN / beta toxin / hemolysin / sphingomyelinase
Function / homology
Function and homology information


sphingomyelin metabolic process / sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region / metal ion binding / cytoplasm
Similarity search - Function
Sphingomyelin phosphodiesterase 2-like / Sphingomyelinase C/phospholipase C / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Endonuclease/exonuclease/phosphatase superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHuseby, M. / Shi, K. / Kruse, A.C. / Ohlendorf, D.H.
Citation
Journal: to be published
Title: Structure and biological functions of beta toxin from Staphylococcus aureus: Role of the hydrophobic beta hairpin in virulence
Authors: Huseby, M. / Shi, K. / Kruse, A.C. / Digre, J. / Mengistu, F. / Bohach, G.A. / Schlievert, P.S. / Ohlendorf, D.H. / Earhart, C.A.
#1: Journal: J.Bacteriol. / Year: 2007
Title: Structure and biological activities of beta toxin from Staphylococcus aureus.
Authors: Huseby, M. / Shi, K. / Brown, C.K. / Digre, J. / Mengistu, F. / Seo, K.S. / Bohach, G.A. / Schlievert, P.M. / Ohlendorf, D.H. / Earhart, C.A.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-hemolysin
B: Beta-hemolysin


Theoretical massNumber of molelcules
Total (without water)72,1842
Polymers72,1842
Non-polymers00
Water9,656536
1
A: Beta-hemolysin


Theoretical massNumber of molelcules
Total (without water)36,0921
Polymers36,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hemolysin


Theoretical massNumber of molelcules
Total (without water)36,0921
Polymers36,0921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.176, 68.668, 127.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-hemolysin


Mass: 36092.156 Da / Num. of mol.: 2 / Fragment: UNP residues 35-330 / Mutation: F310A, P311A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: RN4220 / Gene: hlb / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7LAI8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, 0.1 M MES, VAPOR DIFFUSION, SITTING DROP, temperature 291K
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008 / Details: mirrors
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 1.75→26.18 Å / Num. all: 56896 / Num. obs: 54177 / % possible obs: 93.5 %

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-3000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native Beta Toxin

Resolution: 1.75→26.18 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.887 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2741 5.1 %RANDOM
Rwork0.201 ---
obs0.204 51436 95.35 %-
all-54177 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.83 Å2 / Biso mean: 26.598 Å2 / Biso min: 7.77 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→26.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4656 0 0 536 5192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224775
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.946465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75625.508236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78315824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0471510
X-RAY DIFFRACTIONr_chiral_restr0.1320.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023680
X-RAY DIFFRACTIONr_nbd_refined0.2480.22335
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2501
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4030.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.240
X-RAY DIFFRACTIONr_mcbond_it1.1091.52964
X-RAY DIFFRACTIONr_mcangle_it1.80524670
X-RAY DIFFRACTIONr_scbond_it2.41932111
X-RAY DIFFRACTIONr_scangle_it3.3734.51795
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 131 -
Rwork0.262 2518 -
all-2649 -
obs-101357 63.91 %

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