[English] 日本語
Yorodumi
- PDB-6z17: PqsR (MvfR) in complex with antagonist 6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6z17
TitlePqsR (MvfR) in complex with antagonist 6
ComponentsTranscriptional regulator MvfR
KeywordsDNA BINDING PROTEIN / Pseudomonas aeruginosa / Antagonist / Quorum sensing
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-Q4W / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsRichardson, W.K. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Novel quinazolinone inhibitors of the Pseudomonas aeruginosa quorum sensing transcriptional regulator PqsR.
Authors: Grossman, S. / Soukarieh, F. / Richardson, W. / Liu, R. / Mashabi, A. / Emsley, J. / Williams, P. / Camara, M. / Stocks, M.J.
History
DepositionMay 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0712
Polymers26,7491
Non-polymers3221
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10060 Å2
Unit cell
Length a, b, c (Å)120.266, 120.266, 115.038
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Transcriptional regulator MvfR


Mass: 26749.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Gene: mvfR, PA14_51340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z7A6
#2: Chemical ChemComp-Q4W / 6-chloranyl-3-[(2-propan-2-yl-2,3-dihydro-1,3-thiazol-4-yl)methyl]quinazolin-4-one


Mass: 321.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16ClN3OS / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.38 Å3/Da / Density % sol: 71.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Sodium citrate, 200 mM Ammonium acetate, 5% MPD

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.15→60.13 Å / Num. obs: 8476 / % possible obs: 95.7 % / Redundancy: 10.1 % / CC1/2: 0.97 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.9
Reflection shellResolution: 3.15→3.37 Å / Rmerge(I) obs: 0.803 / Num. unique obs: 1514 / CC1/2: 0.966

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q7w, 4jvc

6q7w

4jvc


Resolution: 3.15→60.13 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.944 / SU B: 17.08 / SU ML: 0.282 / Cross valid method: FREE R-VALUE / ESU R: 0.642 / ESU R Free: 0.352
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2411 406 4.79 %
Rwork0.1953 8070 -
all0.198 --
obs-8476 94.524 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 131.882 Å2
Baniso -1Baniso -2Baniso -3
1-4.972 Å22.486 Å20 Å2
2--4.972 Å20 Å2
3----16.129 Å2
Refinement stepCycle: LAST / Resolution: 3.15→60.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 21 0 1619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171531
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6362243
X-RAY DIFFRACTIONr_angle_other_deg1.2941.5683536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2885202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.29521.30492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25915275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5681514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021853
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
X-RAY DIFFRACTIONr_nbd_refined0.2250.2375
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.21541
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2801
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2859
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3280.216
X-RAY DIFFRACTIONr_nbd_other0.2460.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3060.24
X-RAY DIFFRACTIONr_mcbond_it11.96813.892811
X-RAY DIFFRACTIONr_mcbond_other11.97313.889809
X-RAY DIFFRACTIONr_mcangle_it16.01420.8511012
X-RAY DIFFRACTIONr_mcangle_other16.00920.8511012
X-RAY DIFFRACTIONr_scbond_it12.87914.64839
X-RAY DIFFRACTIONr_scbond_other12.87314.638840
X-RAY DIFFRACTIONr_scangle_it18.01621.631231
X-RAY DIFFRACTIONr_scangle_other18.00821.6291232
X-RAY DIFFRACTIONr_lrange_it22.707266.6826651
X-RAY DIFFRACTIONr_lrange_other22.705266.6546652
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.2320.425150.31600X-RAY DIFFRACTION95.7944
3.232-3.320.31300.287577X-RAY DIFFRACTION95.8926
3.32-3.4160.272280.262558X-RAY DIFFRACTION95.7516
3.416-3.5210.315210.236539X-RAY DIFFRACTION95.5631
3.521-3.6370.296310.22529X-RAY DIFFRACTION95.8904
3.637-3.7640.252310.198497X-RAY DIFFRACTION95.3069
3.764-3.9060.267230.199485X-RAY DIFFRACTION95.1311
3.906-4.0660.282300.2474X-RAY DIFFRACTION95.2741
4.066-4.2460.18200.194455X-RAY DIFFRACTION94.6215
4.246-4.4530.268300.145431X-RAY DIFFRACTION94.4672
4.453-4.6940.186200.137411X-RAY DIFFRACTION94.7253
4.694-4.9780.217240.157395X-RAY DIFFRACTION94.3694
4.978-5.3210.168120.168370X-RAY DIFFRACTION93.6275
5.321-5.7460.229290.211344X-RAY DIFFRACTION93.4837
5.746-6.2930.358190.22311X-RAY DIFFRACTION92.9577
6.293-7.0330.245130.173299X-RAY DIFFRACTION92.8571
7.033-8.1160.27150.162264X-RAY DIFFRACTION92.1233
8.116-9.9280.13190.154233X-RAY DIFFRACTION91.6667
9.928-13.9880.26670.164185X-RAY DIFFRACTION91.4286
13.988-60.130.25590.412113X-RAY DIFFRACTION89.7059

+
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://pdbjlvh1.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