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- PDB-3lkf: LEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS WITH PHOSPHOCHOLIN... -

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Basic information

Entry
Database: PDB / ID: 3lkf
TitleLEUKOCIDIN F (HLGB) FROM STAPHYLOCOCCUS AUREUS WITH PHOSPHOCHOLINE BOUND
ComponentsLEUKOCIDIN F SUBUNIT
KeywordsTOXIN / LEUKOTOXIN / HEMOLYSIN / PORE-FORMING TOXIN
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
PHOSPHOCHOLINE / Gamma-hemolysin component B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOlson, R. / Nariya, H. / Yokota, K. / Kamio, Y. / Gouaux, J.E.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Crystal structure of staphylococcal LukF delineates conformational changes accompanying formation of a transmembrane channel.
Authors: Olson, R. / Nariya, H. / Yokota, K. / Kamio, Y. / Gouaux, E.
History
DepositionJul 28, 1998Processing site: BNL
Revision 1.0Jul 28, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUKOCIDIN F SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2752
Polymers34,0911
Non-polymers1841
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.970, 48.600, 148.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LEUKOCIDIN F SUBUNIT / LUKF / HLGB


Mass: 34090.719 Da / Num. of mol.: 1 / Fragment: WATER-SOLUBLE MONOMER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: SMITH 5R / Gene: LUKF / Plasmid: PTRCLUKF / Gene (production host): LUKF / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P0A077
#2: Chemical ChemComp-PC / PHOSPHOCHOLINE


Mass: 184.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H15NO4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.11 Å3/Da / Density % sol: 45 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125-30 %(w/v)PEG30001reservoir
20.1 MTris1reservoir
34-10 mg/mlprotein1drop
430 mMHEPES1drop
580 mM1dropNaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9184
DetectorType: ADSC / Detector: CCD / Date: Jun 1, 1998 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 26850 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.049
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.176 / % possible all: 86
Reflection
*PLUS
Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 86 % / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PREVIOUSLY DETERMINED STRUCTURE

Resolution: 1.9→6 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1109 5 %RANDOM
Rwork0.199 ---
obs0.199 22172 97 %-
Displacement parametersBiso mean: 11.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 11 253 2616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.17
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.261
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 26815
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 11.017 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.176
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.261

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