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- PDB-2qk7: A covalent S-F heterodimer of staphylococcal gamma-hemolysin -

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Basic information

Entry
Database: PDB / ID: 2qk7
TitleA covalent S-F heterodimer of staphylococcal gamma-hemolysin
Components
  • Gamma-hemolysin component A
  • Gamma-hemolysin component B
KeywordsTOXIN / pore-forming toxin / beta-barrel / protein-protein interaction / molecular plasticity / covalent complex / Cytolysis / Hemolysis / Secreted
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / extracellular region
Similarity search - Function
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
Gamma-hemolysin component A / Gamma-hemolysin component B / F component of leucocodin R
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsRoblin, P. / Guillet, V. / Maveyraud, L. / Mourey, L.
Citation
Journal: Proteins / Year: 2008
Title: A covalent S-F heterodimer of leucotoxin reveals molecular plasticity of beta-barrel pore-forming toxins.
Authors: Roblin, P. / Guillet, V. / Joubert, O. / Keller, D. / Erard, M. / Maveyraud, L. / Prevost, G. / Mourey, L.
#1: Journal: BIOCHEM.J. / Year: 2006
Title: Engineered covalent leucotoxin heterodimers form functional pores: insights into S-F interactions
Authors: Joubert, O. / Viero, G. / Keller, D. / Martinez, E. / Colin, D.A. / Monteil, H. / Mourey, L. / Dalla Serra, M. / Prevost, G.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 20, 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 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999sequence Author stated that these residues are conflicts between different sequence references.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-hemolysin component A
B: Gamma-hemolysin component B


Theoretical massNumber of molelcules
Total (without water)67,6062
Polymers67,6062
Non-polymers00
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.000, 140.000, 73.078
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsThe disulfide linked gamma-hemolysin heterodimer was prepared from variants HlgA T28C and HlgB N156C as described in Joubert et al., Biochem. J. (2006) 396, 381-389. The asymmetric unit contains the heterodimer.

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Components

#1: Protein Gamma-hemolysin component A / H-gamma-2 / H-gamma-II


Mass: 32725.838 Da / Num. of mol.: 1 / Mutation: T57C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: hlgA, hlg2 / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A074
#2: Protein Gamma-hemolysin component B / H-gamma-1 / H-gamma-I


Mass: 34880.570 Da / Num. of mol.: 1 / Mutation: N182C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Species: Staphylococcus aureus / Strain: MW2 / Gene: hlgB / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A077, UniProt: Q57227*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: covalent complex concentrated to 9 mg/ml in 50 mM MES-NaOH, 50 mM NaCl, pH 6.5. Needle and rod shape like crystals obtained in drops prepared by mixing two volumes of protein and one volume ...Details: covalent complex concentrated to 9 mg/ml in 50 mM MES-NaOH, 50 mM NaCl, pH 6.5. Needle and rod shape like crystals obtained in drops prepared by mixing two volumes of protein and one volume of reservoir solution containing 10% polyethylene glycol 8000, 0.05 M Na citrate, pH 5.5. Reservoir volumes of 500 mul used, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorDate: Feb 16, 2005
RadiationMonochromator: Diamond (111), Ge(220) monochromator Sagitally focusing Ge(220) and a multilayer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→50.5 Å / Num. all: 32122 / Num. obs: 32122 / % possible obs: 100 % / Redundancy: 7 % / Rsym value: 0.078 / Net I/σ(I): 8
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.318 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1LKF, 1T5R

1lkf

1t5r


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.109 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.262 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1625 5.1 %RANDOM
Rwork0.17953 ---
obs0.1825 30458 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 46.121 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 0 0 173 4476
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0281.9295964
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8495539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23925.047212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36615717
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2341514
X-RAY DIFFRACTIONr_chiral_restr0.1350.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023373
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21735
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22865
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2263
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.238
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2571.52782
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.15324359
X-RAY DIFFRACTIONr_scbond_it3.30131899
X-RAY DIFFRACTIONr_scangle_it4.8614.51605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 127 -
Rwork0.207 2222 -
obs--99.96 %

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