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- PDB-4ng2: Crystal structure of LasR LBD-QslA complex from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4ng2
TitleCrystal structure of LasR LBD-QslA complex from Pseudomonas aeruginosa
Components
  • Transcriptional activator protein LasR
  • Uncharacterized protein
KeywordsTranscription Regulator / Quorum sensing / antiactivator
Function / homology
Function and homology information


positive regulation of elastin biosynthetic process / regulation of elastin catabolic process / quorum sensing / DNA-binding transcription activator activity / protein-DNA complex / regulation of gene expression / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
LasR-specific antiactivator QslA / LasR-specific antiactivator QslA / 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 ...LasR-specific antiactivator QslA / LasR-specific antiactivator QslA / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / Transcriptional activator protein LasR / LasR-specific antiactivator QslA domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.413 Å
AuthorsFan, H. / Wu, D.H. / Song, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing
Authors: Fan, H. / Dong, Y. / Wu, D.H. / Bowler, M.W. / Zhang, L. / Song, H.
History
DepositionNov 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator protein LasR
B: Transcriptional activator protein LasR
C: Transcriptional activator protein LasR
D: Transcriptional activator protein LasR
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,88816
Polymers184,69812
Non-polymers1,1904
Water5,152286
1
A: Transcriptional activator protein LasR
E: Uncharacterized protein
F: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4724
Polymers46,1743
Non-polymers2971
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-33 kcal/mol
Surface area15350 Å2
MethodPISA
2
B: Transcriptional activator protein LasR
G: Uncharacterized protein
H: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4724
Polymers46,1743
Non-polymers2971
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area15710 Å2
MethodPISA
3
C: Transcriptional activator protein LasR
I: Uncharacterized protein
J: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4724
Polymers46,1743
Non-polymers2971
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-33 kcal/mol
Surface area15740 Å2
MethodPISA
4
D: Transcriptional activator protein LasR
K: Uncharacterized protein
L: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4724
Polymers46,1743
Non-polymers2971
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-34 kcal/mol
Surface area15320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.507, 185.887, 56.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Transcriptional activator protein LasR


Mass: 20627.162 Da / Num. of mol.: 4
Fragment: LasR ligand binding domain (LBD), UNP residues 1-170
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: lasR / Production host: Escherichia coli (E. coli) / References: UniProt: P25084
#2: Protein
Uncharacterized protein / QslA


Mass: 12773.665 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA1244 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I494
#3: Chemical
ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


Mass: 297.390 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H27NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 1K, 0.2M MgCl2, 0.1M NaCl, 50mM sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.41→48.033 Å / Num. all: 64498 / Num. obs: 64498 / % possible obs: 96.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.41→2.54 Å / % possible all: 78

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UV0

2uv0


Resolution: 2.413→48.033 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7728 / SU ML: 0.4 / σ(F): 1 / Phase error: 29.93 / Stereochemistry target values: ML
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 3260 5.07 %Random
Rwork0.2314 ---
all0.2337 ---
obs0.2337 64431 93.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.346 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 195.76 Å2 / Biso mean: 52.9113 Å2 / Biso min: 9.89 Å2
Baniso -1Baniso -2Baniso -3
1--3.7573 Å20 Å20 Å2
2--2.3936 Å2-0 Å2
3---2.6816 Å2
Refinement stepCycle: LAST / Resolution: 2.413→48.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10788 0 84 286 11158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111152
X-RAY DIFFRACTIONf_angle_d1.32515156
X-RAY DIFFRACTIONf_chiral_restr0.0821636
X-RAY DIFFRACTIONf_plane_restr0.0081972
X-RAY DIFFRACTIONf_dihedral_angle_d18.5884136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4134-2.49970.37723640.32076141650551
2.4997-2.59980.32225750.2814109701154591
2.5998-2.71810.33246510.27751202512676100
2.7181-2.86140.33886100.27531206412674100
2.8614-3.04060.31696430.26411204712690100
3.0406-3.27530.32295890.27121211412703100
3.2753-3.60480.28536250.24331204212667100
3.6048-4.12620.24996300.20671202812658100
4.1262-5.19760.23717200.18431193012650100
5.1976-48.04230.22536470.1903119391258699

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