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- PDB-6u3f: Structure-based discovery of a novel small-molecule inhibitor of ... -

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Basic information

Entry
Database: PDB / ID: 6u3f
TitleStructure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus
ComponentsPanton-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
fos-choline-14 / Panton-Valentine Leucocidin F
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 21, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4475
Polymers34,4941
Non-polymers9534
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-20 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.249, 49.249, 266.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 380.523 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H43NO4P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10 mg/mL protein in 10 mM sodium acetate, pH 5.4, 10 mM Fos-Choline 14, 30 mM beta-OG against reservoir solution of 2.6 M ammonium sulfate, 5% PEG400, 0.1 M HEPES, pH 8.5

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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: 1.78→89 Å / Num. obs: 37358 / % possible obs: 99.7 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.9
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 20 / Num. unique obs: 2428 / CC1/2: 0.997 / % possible all: 98.2

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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 1PVL

1pvl


Resolution: 1.78→38.49 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.796 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1887 5.1 %RANDOM
Rwork0.1776 ---
obs0.1792 35471 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 110.17 Å2 / Biso mean: 29.861 Å2 / Biso min: 15.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å2-0 Å2
3----2.17 Å2
Refinement stepCycle: final / Resolution: 1.78→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2389 0 35 192 2616
Biso mean--50.45 37.66 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122475
X-RAY DIFFRACTIONr_angle_refined_deg2.4381.6543347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9645291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01324.234137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02715432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5159
X-RAY DIFFRACTIONr_chiral_restr0.2030.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021893
LS refinement shellResolution: 1.78→1.827 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 166 -
Rwork0.154 2520 -
all-2686 -
obs--98.86 %
Refinement TLS params.Method: refined / Origin x: 13.406 Å / Origin y: 45.832 Å / Origin z: 278.722 Å
111213212223313233
T0.0201 Å20.0116 Å2-0.0067 Å2-0.0509 Å20.0104 Å2--0.0094 Å2
L0.1561 °20.1536 °20.0267 °2-0.2097 °2-0.142 °2--1.3897 °2
S0.0193 Å °-0.0168 Å °-0.0176 Å °0.0093 Å °-0.01 Å °0.0002 Å °-0.0068 Å °0.1165 Å °-0.0093 Å °

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