[English] 日本語
Yorodumi
- PDB-6cc0: Crystal structure of QscR bound to C12-homoserine lactone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6cc0
TitleCrystal structure of QscR bound to C12-homoserine lactone
ComponentsLuxR family transcriptional regulator
KeywordsTRANSCRIPTION / LuxR-type AHL receptor / Pseudomonas aeruginosa QscR
Function / homology
Function and homology information


negative regulation of secondary metabolite biosynthetic process / quorum sensing / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector ...Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain / Transcription factor LuxR-like, autoinducer-binding domain superfamily / Autoinducer binding domain / LuxR-type HTH domain signature. / LuxR-type HTH domain profile. / Transcription regulator LuxR, C-terminal / Bacterial regulatory proteins, luxR family / helix_turn_helix, Lux Regulon / Signal transduction response regulator, C-terminal effector / Beta-Lactamase / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-[(3S)-2-oxooxolan-3-yl]dodecanamide / LuxR family transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChurchill, M.E.A. / Wysoczynski-Horita, C.L.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM109403 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA046934 United States
National Institutes of Health/Office of the DirectorS10OD012033 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)UL1TR001082 United States
National Institutes of Health/Office of the DirectorS10OD12073 United States
National Science Foundation (NSF, United States)DMR-1121288 United States
CitationJournal: Mol. Microbiol. / Year: 2018
Title: Mechanism of agonism and antagonism of the Pseudomonas aeruginosa quorum sensing regulator QscR with non-native ligands.
Authors: Wysoczynski-Horita, C.L. / Boursier, M.E. / Hill, R. / Hansen, K. / Blackwell, H.E. / Churchill, M.E.A.
History
DepositionFeb 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LuxR family transcriptional regulator
B: LuxR family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1374
Polymers54,5702
Non-polymers5672
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-21 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.591, 91.910, 93.999
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein LuxR family transcriptional regulator / PhzR / Quorum-sensing control repressor / Regulatory protein SdiA


Mass: 27285.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain A N-terminal MHD not visible Chain B N-terminal MHDE not visible
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: phzR, qscR, sdiA_2, CAZ03_14830, CAZ10_26210, DC19_16645, HQ52_16845, PAERUG_E15_London_28_01_14_06284, PAMH19_5306
Production host: Escherichia coli (E. coli) / References: UniProt: Q9RMS5
#2: Chemical ChemComp-EWM / N-[(3S)-2-oxooxolan-3-yl]dodecanamide


Mass: 283.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H29NO3 / Details: C12-L-homoserine lactone / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.04 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate, 20 w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→48.802 Å / Num. obs: 20134 / % possible obs: 94.9 % / Redundancy: 4 % / Net I/σ(I): 11.8
Reflection shellResolution: 2.48→2.63 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2797 / CC1/2: 0.807 / % possible all: 96.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3szt
Resolution: 2.5→48.802 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.18 / Phase error: 29.28
RfactorNum. reflection% reflection
Rfree0.2699 840 5 %
Rwork0.2085 --
obs0.2116 16808 94.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 40 51 3884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074009
X-RAY DIFFRACTIONf_angle_d0.8655434
X-RAY DIFFRACTIONf_dihedral_angle_d12.9232353
X-RAY DIFFRACTIONf_chiral_restr0.05580
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.65660.39761360.31362629X-RAY DIFFRACTION95
2.6566-2.86180.34571400.28262625X-RAY DIFFRACTION94
2.8618-3.14970.34251380.2542694X-RAY DIFFRACTION96
3.1497-3.60530.31631410.22742647X-RAY DIFFRACTION94
3.6053-4.54180.24521370.17432660X-RAY DIFFRACTION94
4.5418-48.81120.19161480.16522713X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.07120.0087-0.02110.0092-0.03280.22180.0279-0.14480.40720.10850.0843-0.1588-0.1932-0.02180.020.49130.4112-0.09840.325-0.16910.4652-76.76769.571716.5882
20.41780.11280.31650.19090.20270.35460.0302-0.1333-0.14430.21280.0322-0.09380.031-0.41460.00230.00480.0966-0.03650.34220.01510.309-77.0951-10.939415.3987
30.1373-0.1430.0980.228-0.09840.08130.246-0.1171-0.2305-0.0507-0.10840.05940.2118-0.1767-0.01350.1183-0.0941-0.18890.55660.06370.1948-80.1113-14.38543.6143
40.0578-0.0387-0.06830.2086-0.07530.15770.0578-0.0053-0.0680.0075-0.01730.077-0.095-0.09470.32580.08930.0819-0.12080.3396-0.00930.1147-75.4474-3.68787.6264
50.8003-0.0478-0.27410.0041-0.0080.79360.1142-0.05440.287-0.10620.1713-0.0565-0.2808-0.0470.28680.43740.0258-0.0630.10650.02810.2019-71.30983.825910.6855
60.05730.00220.00560.0922-0.1110.29340.0417-0.05950.020.30670.0137-0.1263-0.20080.1442-0.00990.38370.0155-0.09730.12-0.02110.1937-48.8705-8.934128.8921
70.69240.092-0.53390.1844-0.10640.78920.2258-0.10980.00110.2448-0.0302-0.1157-0.37040.00550.330.27950.0304-0.11180.146-0.050.1076-46.5822-15.075531.0332
80.59390.0331-0.33310.72260.16450.5965-0.06540.0070.0425-0.10130.06720.06880.06720.1172-0.00010.08780.02890.03210.10430.04250.1568-48.89436.13445.8823
90.1696-0.0485-0.08280.123-0.02050.1007-0.05460.1578-0.1835-0.05170.0727-0.0031-0.0055-0.202200.161-0.0140.03070.142-0.00490.153-55.1675-26.699116.1549
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 32 )
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 108 )
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 138 )
5X-RAY DIFFRACTION5chain 'A' and (resid 139 through 168 )
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 237 )
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 168 )
9X-RAY DIFFRACTION9chain 'B' and (resid 169 through 237 )

+
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