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- PDB-2uv0: Structure of the P. aeruginosa LasR ligand-binding domain bound t... -

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Basic information

Entry
Database: PDB / ID: 2uv0
TitleStructure of the P. aeruginosa LasR ligand-binding domain bound to its autoinducer
ComponentsTRANSCRIPTIONAL ACTIVATOR PROTEIN LASRActivator (genetics)
KeywordsTRANSCRIPTION / ACYL-HOMOSERINE LACTONE RECEPTOR / QUORUM SENSING / TRANSCRIPTION REGULATION / ALPHA-BETA-ALPHA SANDWICH
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
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBottomley, M.J. / Muraglia, E. / Bazzo, R. / Carfi, A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Molecular Insights Into Quorum Sensing in the Human Pathogen Pseudomonas Aeruginosa from the Structure of the Virulence Regulator Lasr Bound to its Autoinducer.
Authors: Bottomley, M.J. / Muraglia, E. / Bazzo, R. / Carfi, A.
History
DepositionMar 8, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
F: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
G: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
H: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9358
Polymers78,7464
Non-polymers1,1904
Water9,764542
1
E: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
G: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9684
Polymers39,3732
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-5.1 kcal/mol
Surface area14680 Å2
MethodPISA
2
F: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
H: TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9684
Polymers39,3732
Non-polymers5952
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-5.2 kcal/mol
Surface area14810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.820, 85.330, 75.510
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99993, 0.00497, -0.01108), (0.00825, 0.94748, -0.31971), (0.00891, -0.31978, -0.94745)77.41255, 23.80472, 145.88155
2given(-0.99993, 0.00026, 0.01208), (-0.01208, -0.00192, -0.99993), (-0.00024, -1, 0.00192)79.4353, 68.86843, 67.95043

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Components

#1: Protein
TRANSCRIPTIONAL ACTIVATOR PROTEIN LASR / Activator (genetics) / LASR


Mass: 19686.465 Da / Num. of mol.: 4 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 1-173
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1
Description: PSEUDOMONAS GENETIC STOCK CENTER, GREENVILLE, NC, USA
Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25084
#2: Chemical
ChemComp-OHN / N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE


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


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL GLY-ALA IS A REMNANT OF THE AFFINITY- PURIFICATION TAG.

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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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growpH: 7.3
Details: 20% W/V PEG 4000, 80 MM CALCIUM ACETATE, 40 MM HEPES PH 7.3, 5 MM DTT AND 50 MICROMOLAR N-3-OXO-DODECANOYL-HOMOSERINE LACTONE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 21, 2005 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 61495 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 8.1 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.1 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
CNXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→40 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.864 / SU B: 6.189 / SU ML: 0.105 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.149
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. OF THE EXPECTED 175 RESIDUE PER CHAIN, ALL RESIDUES WERE VISIBLE EXCEPT FOR A FEW (USUALLY LESS THAN 5) AT THE N- AND C-TERMINI.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3112 5.1 %RANDOM
Rwork0.209 ---
obs0.211 58208 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20.23 Å2
2--0.32 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5203 0 84 542 5829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225498
X-RAY DIFFRACTIONr_bond_other_d0.0010.023798
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.9647443
X-RAY DIFFRACTIONr_angle_other_deg1.2823.0049076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5555676
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25623.514259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15815890
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7521536
X-RAY DIFFRACTIONr_chiral_restr0.0610.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021190
X-RAY DIFFRACTIONr_nbd_refined0.2030.21358
X-RAY DIFFRACTIONr_nbd_other0.1850.24109
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22723
X-RAY DIFFRACTIONr_nbtor_other0.0850.22789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2230.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.54103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.56225302
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.37132501
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7724.52131
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.37 218
Rwork0.288 4226
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)
12.6333-0.0364-0.59870.68850.04112.22950.03130.30030.0306-0.0116-0.01380.04120.0185-0.1787-0.0174-0.05790.0121-0.01250.0310.0181-0.072224.567711.385477.1832
22.8929-0.8822-0.17821.8350.00591.17920.04290.07930.0929-0.08-0.0501-0.17990.05370.0870.0071-0.07020.00780.0022-0.0808-0.0208-0.048254.47626.31534.8427
31.58010.023-0.54890.6673-0.20872.6264-0.0160.0652-0.0672-0.071-0.0034-0.02720.120.14930.0194-0.04130.0336-0.01120.04910.0051-0.055151.83289.614269.2762
42.411-0.8024-0.33481.90660.53831.3223-0.0395-0.1324-0.14530.08880.02110.22860.0256-0.09490.0184-0.06920.00030.0024-0.0879-0.0026-0.027625.119232.436641.8901
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1E6 - 168
2X-RAY DIFFRACTION2F5 - 168
3X-RAY DIFFRACTION3G2 - 167
4X-RAY DIFFRACTION4H2 - 168

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