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- PDB-6u3y: Structure-based discovery of a novel small-molecule inhibitor of ... -

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Basic information

Entry
Database: PDB / ID: 6u3y
TitleStructure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
Components
  • Gamma-hemolysin subunit A
  • Panton-Valentine Leucocidin F
KeywordsTOXIN / alpha-toxin / PVL / Leukocidins / MRSA
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
ACETATE ION / fos-choline-14 / Gamma-hemolysin subunit A / Panton-Valentine Leucocidin F
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLiu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence.
Authors: Liu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Panton-Valentine Leucocidin F
B: Gamma-hemolysin subunit A
D: Gamma-hemolysin subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,39430
Polymers99,2433
Non-polymers3,15127
Water6,287349
1
A: Panton-Valentine Leucocidin F
B: Gamma-hemolysin subunit A
hetero molecules

A: Panton-Valentine Leucocidin F
B: Gamma-hemolysin subunit A
hetero molecules

A: Panton-Valentine Leucocidin F
B: Gamma-hemolysin subunit A
hetero molecules

A: Panton-Valentine Leucocidin F
B: Gamma-hemolysin subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)277,53788
Polymers267,4758
Non-polymers10,06280
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area49350 Å2
ΔGint-547 kcal/mol
Surface area94510 Å2
MethodPISA
2
D: Gamma-hemolysin subunit A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0108
Polymers32,3751
Non-polymers6357
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-87 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.097, 139.097, 246.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

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Protein , 2 types, 3 molecules ABD

#1: Protein Panton-Valentine Leucocidin F / Panton-Valentine leukocidin chain F / Panton-Valentine leukocidin chain F protein / Panton- ...Panton-Valentine leukocidin chain F / Panton-Valentine leukocidin chain F protein / Panton-valentine Leukocidin F


Mass: 34494.039 Da / Num. of mol.: 1 / Fragment: UNP residues 25-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: lukF-PV, hlgB_1, lukF- PV, LukPV-F, lukPV-F, lukPVF, NCTC6133_01921
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q5FBD2
#2: Protein Gamma-hemolysin subunit A / LukS-PV / Panton-Valentine leucocidin S / Panton-valentine Leukocidin S


Mass: 32374.668 Da / Num. of mol.: 2 / Fragment: UNP residues 29-312
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: lukS-PV, LukPV-S, lukPV-S, lukPVS, EP54_02590, EQ90_09955
Production host: Escherichia coli K-12 (bacteria) / References: UniProt: B1Q017

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Non-polymers , 4 types, 376 molecules

#3: Chemical ChemComp-PQJ / fos-choline-14 / tetradecyl 2-(trimethyl-$l^{4}-azanyl)ethyl hydrogen phosphate


Mass: 380.523 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H43NO4P
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 6.7 mg/mL LukF-PV, 6.3 mg/mL LukS-PV, 10 mM sodium acetate, pH 5.4, 15 mM Fos-Choline-14, 40 mM beta-OG against reservoir solution of 0.16 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→38.7 Å / Num. obs: 76882 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.956 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.6
Reflection shellResolution: 2.04→2.09 Å / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3741 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B07

3b07


Resolution: 2.04→38.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.954 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.146 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3889 5.1 %RANDOM
Rwork0.1823 ---
obs0.1845 72993 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.19 Å2 / Biso mean: 44.123 Å2 / Biso min: 21.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å2-0 Å2-0 Å2
2---1.38 Å2-0 Å2
3---2.76 Å2
Refinement stepCycle: final / Resolution: 2.04→38.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 159 349 7154
Biso mean--67.88 47.48 -
Num. residues----816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0126941
X-RAY DIFFRACTIONr_angle_refined_deg2.2391.6519388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.045810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65423.88384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.567151173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6741527
X-RAY DIFFRACTIONr_chiral_restr0.1670.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.025342
LS refinement shellResolution: 2.04→2.092 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.269 270 -
Rwork0.242 5272 -
obs--98.66 %
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)
10.1905-0.05580.07250.28940.08850.1302-0.0021-0.02560.02850.0247-0.003-0.03980.02270.0040.00510.0798-0.0005-0.00240.0721-0.00280.05829.8129126.551773.1177
20.1585-0.0424-0.02650.21160.11180.25110.0049-0.02960.00390.0226-0.0057-0.0243-0.00140.02060.00070.0865-0.0024-0.00840.07360.01150.054130.8414150.484673.047
30.34010.1330.29890.34330.04132.17030.0926-0.1940.00250.144-0.12940.04530.12110.050.03680.1625-0.10740.01170.26230.00660.00950.9828158.5826113.8134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 301
2X-RAY DIFFRACTION2B5 - 284
3X-RAY DIFFRACTION3D11 - 284

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