[English] 日本語
Yorodumi
- PDB-6u3f: Structure-based discovery of a novel small-molecule inhibitor of ... -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 °

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more