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- PDB-6d6p: The structure of ligand binding domain of LasR in complex with TP... -

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Basic information

Entry
Database: PDB / ID: 6d6p
TitleThe structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 19
ComponentsTranscriptional activator protein LasR
Keywordssignaling protein/agonist / LuxR receptor / signaling protein-agonist complex
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
Chem-FY1 / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å
AuthorsDong, S.H. / Nair, S.K.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural and Biochemical Studies of Non-native Agonists of the LasR Quorum-Sensing Receptor Reveal an L3 Loop "Out" Conformation for LasR.
Authors: O'Reilly, M.C. / Dong, S.H. / Rossi, F.M. / Karlen, K.M. / Kumar, R.S. / Nair, S.K. / Blackwell, H.E.
History
DepositionApr 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9308
Polymers76,0344
Non-polymers1,8964
Water8,017445
1
A: Transcriptional activator protein LasR
B: Transcriptional activator protein LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9654
Polymers38,0172
Non-polymers9482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area16360 Å2
MethodPISA
2
C: Transcriptional activator protein LasR
D: Transcriptional activator protein LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9654
Polymers38,0172
Non-polymers9482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area16120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.130, 84.610, 77.170
Angle α, β, γ (deg.)90.00, 101.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional activator protein LasR


Mass: 19008.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: lasR, PA1430 / Production host: Escherichia coli (E. coli) / References: UniProt: P25084
#2: Chemical
ChemComp-FY1 / N-{[3,5-dibromo-2-(methoxymethoxy)phenyl]methyl}-2-nitrobenzamide


Mass: 474.101 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14Br2N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 80 mM calcium acetate, 40 mM HEPES (pH 7.3), 3 mM dithiothreitol, and 16% polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→25 Å / Num. obs: 80637 / % possible obs: 99.9 % / Redundancy: 4.6 % / Net I/σ(I): 11.4
Reflection shellResolution: 1.65→1.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
UCSD-systemdata processing
XDSdata scaling
PHASERphasing
RefinementResolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.405 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24767 4244 5 %RANDOM
Rwork0.21875 ---
obs0.22019 80637 99.9 %-
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: 28.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20.91 Å2
2--0.65 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: 1 / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5287 0 25 445 5757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195475
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9717421
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.55660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42323.658257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1915863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.321532
X-RAY DIFFRACTIONr_chiral_restr0.0670.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214274
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 311 -
Rwork0.294 5920 -
obs--99.89 %

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