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- PDB-1pvl: STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN F COMPONENT FROM STA... -

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Basic information

Entry
Database: PDB / ID: 1pvl
TitleSTRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN F COMPONENT FROM STAPHYLOCOCCUS AUREUS
ComponentsLEUCOCIDIN
KeywordsLEUCOTOXIN / BI-COMPONENT LEUCOTOXIN / TRANSMEMBRANE PORE
Function / homology
Function and homology information


cytolysis in another organism / : / 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
LukF-PV / Panton-Valentine Leucocidin F
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsPedelacq, J.D. / Mourey, L. / Maveyraud, L. / Prevost, G. / Samama, J.P.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: The structure of a Staphylococcus aureus leucocidin component (LukF-PV) reveals the fold of the water-soluble species of a family of transmembrane pore-forming toxins.
Authors: Pedelacq, J.D. / Maveyraud, L. / Prevost, G. / Baba-Moussa, L. / Gonzalez, A. / Courcelle, E. / Shepard, W. / Monteil, H. / Samama, J.P. / Mourey, L.
History
DepositionJan 12, 1999Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEUCOCIDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8853
Polymers34,4941
Non-polymers3902
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.740, 72.380, 98.930
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 LEUCOCIDIN / LUKF-PV


Mass: 34494.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Cellular location: CHROMOSOME / Strain: V8 / References: UniProt: O50604, UniProt: Q5FBD2*PLUS
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.65 Å3/Da / Density % sol: 53.1 %
Crystal growpH: 6.8 / Details: pH 6.8
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
2200 mMTris-HCl1reservoir
421 %(w/v)PEG40001reservoir
57 mMcadmium chloride1reservoir
3MES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.8270, 1.1271
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8271
21.12711
ReflectionResolution: 2→24.4 Å / Num. obs: 21089 / % possible obs: 85 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.06 / Net I/σ(I): 8
Reflection shellResolution: 2→2.12 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 7.2 / Rsym value: 0.101 / % possible all: 88
Reflection
*PLUS
Num. measured all: 96992
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2→24.4 Å / SU B: 2.36 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1080 5 %RANDOM
Rwork0.2012 ---
obs-21049 85 %-
Displacement parametersBiso mean: 15.3 Å2
Refinement stepCycle: LAST / Resolution: 2→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 24 168 2593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0270.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.05
X-RAY DIFFRACTIONp_mcbond_it0.8441.5
X-RAY DIFFRACTIONp_mcangle_it1.0241
X-RAY DIFFRACTIONp_scbond_it1.6881.5
X-RAY DIFFRACTIONp_scangle_it2.6563
X-RAY DIFFRACTIONp_plane_restr0.00980.02
X-RAY DIFFRACTIONp_chiral_restr0.1550.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2420.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1630.3
X-RAY DIFFRACTIONp_planar_tor1.41.5
X-RAY DIFFRACTIONp_staggered_tor10.95
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor27.97.5
X-RAY DIFFRACTIONp_special_tor5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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