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- PDB-6cc0: Crystal structure of QscR bound to C12-homoserine lactone -

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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


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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


Mass: 18.015 Da / Num. of mol.: 51 / 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: 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

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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

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3szt

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

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)
10.07120.0087-0.02110.0092-0.03280.22180.0279-0.14480.40720.10850.0843-0.1588-0.1932-0.02180.020.49130.4112-0.09840.325-0.16910.4652-76.76769.571716.5882
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 )

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