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- PDB-3szt: Quorum Sensing Control Repressor, QscR, Bound to N-3-oxo-dodecano... -

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Basic information

Entry
Database: PDB / ID: 3szt
TitleQuorum Sensing Control Repressor, QscR, Bound to N-3-oxo-dodecanoyl-L-Homoserine Lactone
ComponentsQuorum-sensing control repressor
KeywordsTRANSCRIPTION / quorum sensing acyl-homoserine lactone / Helix-turn-Helix / Transcription Factor / 3-oxo-C12 HSL
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-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / LuxR family transcriptional regulator
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsChurchill, M.E.A. / Lintz, M.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of QscR, a Pseudomonas aeruginosa quorum sensing signal receptor.
Authors: Lintz, M.J. / Oinuma, K. / Wysoczynski, C.L. / Greenberg, E.P. / Churchill, M.E.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quorum-sensing control repressor
B: Quorum-sensing control repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1885
Polymers54,5702
Non-polymers6183
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-21 kcal/mol
Surface area21240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.862, 94.862, 104.953
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Quorum-sensing control repressor / QcsR


Mass: 27285.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PA01 / Gene: PA1898, qscR / Plasmid: pET3a-qscR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: Q9RMS5
#2: Chemical ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H27NO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.5 Å3/Da / Density % sol: 50.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.83
Details: 0.168 M magnesium acetate, 21.8% PEG8000, 0.1 M Tris, pH 7.83, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 22, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 19230 / Num. obs: 19230 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 61.9 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 40
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1882 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
JBluIce-EPICSdata collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SCRWL MODEL OF AHL AND DNA-BINDING DOMAINS OF TRAR

Resolution: 2.55→15 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 22.666 / SU ML: 0.234
Isotropic thermal model: ISOTROPIC WITH TLS GROUP REFINEMENT IN THE LAST REFINEMENT CYCLE
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.724 / ESU R Free: 0.321 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26594 953 5.3 %RANDOM
Rwork0.22264 ---
all0.2249 17116 --
obs0.2249 17116 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 78.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.19 Å20 Å2
2---0.39 Å20 Å2
3---0.58 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.55→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 43 20 3671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223766
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9615103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.145456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.96722.327159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94615609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1151526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2558
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212837
X-RAY DIFFRACTIONr_mcbond_it1.57332274
X-RAY DIFFRACTIONr_mcangle_it2.41643646
X-RAY DIFFRACTIONr_scbond_it1.11721492
X-RAY DIFFRACTIONr_scangle_it1.62131456
LS refinement shellResolution: 2.55→2.614 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 70 -
Rwork0.335 1238 -
obs--99.85 %
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)
110.80375.58237.76762.90444.01825.5888-1.3510.64921.0815-0.69910.45890.7099-0.97580.42520.89221.2663-0.32340.02131.40130.12551.397122.35014.2213-9.0622
23.94083.3252-3.431314.84713.43676.5273-0.45350.1776-0.0465-1.07910.16840.93930.25670.04460.28510.5447-0.0019-0.40150.4892-0.11380.456227.953313.2969-9.9764
33.3935-0.3598-0.39635.3975-1.41712.91910.19840.3859-0.4632-0.8881-0.2131-0.2660.64760.1780.01470.3170.0187-0.01020.1559-0.03610.090741.458914.1037-4.3289
43.68260.53340.4517.0963-0.81273.43840.023-0.0129-0.24470.10420.0486-0.09360.32990.1047-0.07160.08760.0211-0.02580.05210.00640.026639.425920.09582.8287
55.2536-4.227-1.15113.4413.64634.9903-0.04690.1681-0.60150.5559-0.23651.56350.6982-0.98370.28350.3904-0.0993-0.08630.36290.01920.447724.815714.24522.0585
60.6241-1.42860.19753.7522-0.29390.12240.42060.1942-0.2386-1.3217-0.11670.12160.05760.1338-0.30390.98620.0783-0.07230.6804-0.07350.957341.9472-5.1725-4.346
71.1079-2.00371.58363.813-2.75894.72950.01890.0094-0.0755-0.16540.03640.2386-0.07530.2118-0.05530.1716-0.0092-0.04660.07420.01280.084852.0379-17.751715.82
82.4551-2.58411.832712.24150.56222.8207-0.16690.08030.2606-0.60420.06520.1221-0.6370.12320.10160.2766-0.0369-0.0030.09820.00940.102252.2942-13.00846.6793
94.44851.5479-1.3090.906-1.32446.0395-0.2677-0.29430.2560.36770.39730.5634-1.203-1.1199-0.12961.11570.35250.28271.50120.16441.536419.88148.932623.9932
1030.1764-10.0902-2.23223.8608-1.386211.6947-0.4372-0.16520.32870.13540.0491-0.03410.9280.01690.38810.4666-0.09980.05590.33130.0580.646735.7332-3.446920.8441
110.4604-0.66391.82431.3909-1.91758.4485-0.0341-0.2714-0.28650.4340.24981.03110.7105-1.3545-0.21570.9393-0.13640.30791.05660.20651.24327.1741-9.592427.5942
125.95080.7016-4.85292.2938-2.899812.63260.0721-0.2332-0.4505-0.12380.21190.38441.256-0.1646-0.2840.8034-0.2622-0.08240.43160.0620.918427.8503-9.253513.7605
130.606-1.37712.89373.1921-6.606213.96980.206-0.2938-0.194-0.29910.41410.53061.0873-1.1699-0.62011.1623-0.77790.17411.21360.12571.655117.6194-16.593821.1393
141.1303-0.3768-0.975312.0538-1.13084.09410.21930.0641-0.31380.1050.01880.82940.1022-0.7349-0.23810.3715-0.07690.00030.42630.06850.389429.94870.936815.6708
154.7568-1.82242.65883.49061.34463.4949-0.2457-0.6897-0.2657-0.2988-0.4181.101-0.3796-0.99470.66370.835-0.0691-0.10481.26910.13441.256214.98441.655711.1328
168.62011.95890.57521.16920.66710.449-0.1117-1.2550.08340.13220.07570.14180.07580.11910.03590.73750.09640.06430.95240.07820.69938.11167.354823.0504
178.3947-2.3132-0.90954.5683-0.39996.4566-0.40340.01810.4926-0.49090.3258-1.1506-0.97621.19380.07770.5143-0.1480.02660.381-0.11160.475663.3344.949910.3362
188.75240.26453.64866.9651-0.02937.06140.0135-0.59620.090.17130.1259-0.5955-0.3481-0.0207-0.13940.33090.0362-0.030.2462-0.13320.260657.26593.124718.8925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 17
2X-RAY DIFFRACTION2A18 - 32
3X-RAY DIFFRACTION3A33 - 64
4X-RAY DIFFRACTION4A65 - 134
5X-RAY DIFFRACTION5A135 - 160
6X-RAY DIFFRACTION6A161 - 176
7X-RAY DIFFRACTION7A177 - 203
8X-RAY DIFFRACTION8A204 - 237
9X-RAY DIFFRACTION9B6 - 36
10X-RAY DIFFRACTION10B37 - 48
11X-RAY DIFFRACTION11B49 - 69
12X-RAY DIFFRACTION12B70 - 90
13X-RAY DIFFRACTION13B99 - 112
14X-RAY DIFFRACTION14B113 - 130
15X-RAY DIFFRACTION15B131 - 152
16X-RAY DIFFRACTION16B153 - 176
17X-RAY DIFFRACTION17B177 - 203
18X-RAY DIFFRACTION18B204 - 237

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