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- PDB-3i48: Crystal structure of beta toxin from Staphylococcus aureus F277A,... -

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Basic information

Entry
Database: PDB / ID: 3i48
TitleCrystal structure of beta toxin from Staphylococcus aureus F277A, P278A mutant with bound magnesium ions
ComponentsBeta-hemolysin
KeywordsTOXIN / beta toxin / hemolysin / sphingomyelinase
Function / homology
Function and homology information


sphingomyelin phosphodiesterase activity / killing of cells of another organism / extracellular region / metal ion binding
Similarity search - Function
Sphingomyelinase C/phospholipase C / Sphingomyelin phosphodiesterase 2-like / 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
PHOSPHATE ION / Beta-hemolysin
Similarity search - Component
Biological speciesStaphylococcus aureus RN4220 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuseby, M. / Shi, K. / Kruse, A.C. / Ohlendorf, D.H.
Citation
Journal: to be published / Year: 2009
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: 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 / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,4236
Polymers72,1842
Non-polymers2394
Water8,503472
1
A: Beta-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2113
Polymers36,0921
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2113
Polymers36,0921
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 68.577, 126.559
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 RN4220 (bacteria)
Strain: RN2440 / Gene: hlb / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7LAI8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 4000, 0.1 M MES, 5mM MgCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: Oct 11, 2007 / 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: 1.8→50 Å / Num. all: 51464 / Num. obs: 51464 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.055 / Χ2: 1.387 / Net I/σ(I): 11.7
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2493 / Χ2: 0.982 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
CrystalCleardata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I41

3i41


Resolution: 1.8→28.16 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2625 5.1 %RANDOM
Rwork0.184 ---
obs0.185 48742 99.84 %-
all-51405 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.87 Å2 / Biso mean: 28.979 Å2 / Biso min: 13.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 12 472 5150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224794
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9436493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145579
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6725.527237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13515825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5161510
X-RAY DIFFRACTIONr_chiral_restr0.1290.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023692
X-RAY DIFFRACTIONr_nbd_refined0.2130.22344
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23304
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2473
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.229
X-RAY DIFFRACTIONr_mcbond_it1.1161.52891
X-RAY DIFFRACTIONr_mcangle_it1.8724682
X-RAY DIFFRACTIONr_scbond_it2.36731903
X-RAY DIFFRACTIONr_scangle_it3.5324.51811
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 217 -
Rwork0.212 3510 -
all-3727 -
obs--99.41 %

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