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- PDB-3i5v: Crystal structure of beta toxin 275-280 from Staphylococcus aureus -

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Basic information

Entry
Database: PDB / ID: 3i5v
TitleCrystal structure of beta toxin 275-280 from Staphylococcus aureus
ComponentsBeta-hemolysin
KeywordsTOXIN / beta toxin / hemolysin / sphingomyelinase
Function / homology
Function and homology information


sphingomyelin phosphodiesterase activity / phospholipase C / phosphatidylcholine phospholipase C activity / toxin 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
DIACYL GLYCEROL / Beta-hemolysin / Phospholipase C
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Apr 3, 2024Group: 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 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)142,8715
Polymers142,2464
Non-polymers6251
Water2,090116
1
A: Beta-hemolysin


Theoretical massNumber of molelcules
Total (without water)35,5621
Polymers35,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-hemolysin


Theoretical massNumber of molelcules
Total (without water)35,5621
Polymers35,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-hemolysin


Theoretical massNumber of molelcules
Total (without water)35,5621
Polymers35,5621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1872
Polymers35,5621
Non-polymers6251
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.184, 69.053, 75.654
Angle α, β, γ (deg.)93.06, 94.60, 92.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Beta-hemolysin


Mass: 35561.543 Da / Num. of mol.: 4 / Fragment: UNP residues 35-330
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, UniProt: P09978*PLUS
#2: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS IS A DELETION MUTANT DELTA(308-313)/DG, IN WHICH RESIDUES 308-313 HAVE BEEN DELETED AND ...THIS IS A DELETION MUTANT DELTA(308-313)/DG, IN WHICH RESIDUES 308-313 HAVE BEEN DELETED AND REPLACED WITH RESIDUES ASP-GLY.

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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: 2.02 Å3/Da / Density % sol: 38.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15-0.25 M NaF, 28-34% PEG 3350, pH 7.0, 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: 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: 2.8→38.4 Å / Num. all: 22252 / Num. obs: 22252 / % possible obs: 94.97 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.626 Å2
Reflection shellResolution: 2.8→2.99 Å / % possible all: 38.8

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Processing

Software
NameVersionClassificationNB
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Wild-type beta toxin from Staphylococcus aureus

Resolution: 2.8→38.4 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2667 22252 -Random
Rwork0.2141 ---
all0.2141 22252 --
obs0.2141 21132 94.97 %-
Displacement parametersBiso max: 281.22 Å2 / Biso mean: 85.412 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.8→38.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9122 0 17 116 9255
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3722-0.02120.31010.0829-0.55861.31390.0919-0.1645-0.02190.25880.07740.00240.0481-0.1217-0.13290.7739-0.10680.03690.34430.00010.3639-4.0646-23.66721.63
20.23970.0767-0.28590.06840.24122.02820.01260.1663-0.0078-0.11530.0695-0.0085-0.27540.458-0.07910.3629-0.11280.02320.4865-0.01480.329619.63568.072444.2485
3-0.22750.0581-0.0230.2280.14242.9461-0.0438-0.03830.01450.0285-0.00950.0128-0.39380.61010.04720.3059-0.0346-0.00060.39680.00890.318422.398613.56736.6505
40.29040.1228-0.05240.05980.13241.8814-0.0566-0.0238-0.00930.05350.0954-0.00820.4672-0.212-0.02060.4433-0.01640.02840.3030.01660.3241-4.1109-22.1183-16.0242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA9
2X-RAY DIFFRACTION2chain BB9
3X-RAY DIFFRACTION3chain CC9
4X-RAY DIFFRACTION4chain DD9 - 1

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