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- PDB-6d6a: The structure of ligand binding domain of LasR in complex with TP... -

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Basic information

Entry
Database: PDB / ID: 6d6a
TitleThe structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 10
ComponentsTranscriptional activator protein LasR
Keywordssignaling protein/agonist / LuxR receptor / signaling protein-agonist complex
Function / homology
Function and homology information


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-FXD / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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 20, 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
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)156,34116
Polymers152,0688
Non-polymers4,2738
Water11,944663
1
A: Transcriptional activator protein LasR
B: Transcriptional activator protein LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0854
Polymers38,0172
Non-polymers1,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-13 kcal/mol
Surface area15280 Å2
MethodPISA
2
C: Transcriptional activator protein LasR
D: Transcriptional activator protein LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0854
Polymers38,0172
Non-polymers1,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area15440 Å2
MethodPISA
3
E: Transcriptional activator protein LasR
F: Transcriptional activator protein LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0854
Polymers38,0172
Non-polymers1,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-13 kcal/mol
Surface area15260 Å2
MethodPISA
4
G: Transcriptional activator protein LasR
H: Transcriptional activator protein LasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0854
Polymers38,0172
Non-polymers1,0682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-14 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.280, 84.450, 156.200
Angle α, β, γ (deg.)90.00, 95.71, 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.: 8
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-FXD / 2,4-dibromo-6-{[(2-nitrobenzene-1-carbonyl)amino]methyl}phenyl benzoate


Mass: 534.154 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H14Br2N2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 282.1 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 / Ambient temp details: liquid nitrogen air flow
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 102583 / % possible obs: 97.56 % / Redundancy: 3.9 % / Net I/σ(I): 11.7
Reflection shellResolution: 1.9→2 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
UCSD-systemdata processing
XDSdata scaling
PHASERphasing
RefinementResolution: 1.9→38.86 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.321 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22412 5401 5 %RANDOM
Rwork0.17949 ---
obs0.18172 102615 97.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.844 Å2
Baniso -1Baniso -2Baniso -3
1--1.78 Å2-0 Å20.46 Å2
2--1.54 Å20 Å2
3---0.15 Å2
Refinement stepCycle: 1 / Resolution: 1.9→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10451 0 240 663 11354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910989
X-RAY DIFFRACTIONr_bond_other_d0.0020.029804
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.97814890
X-RAY DIFFRACTIONr_angle_other_deg1.166322697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06751317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00423.738511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.836151738
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6221564
X-RAY DIFFRACTIONr_chiral_restr0.1160.21529
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112383
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022445
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_it2.4982.5245292
X-RAY DIFFRACTIONr_mcbond_other2.4952.5245291
X-RAY DIFFRACTIONr_mcangle_it3.6273.7676601
X-RAY DIFFRACTIONr_mcangle_other3.6283.7686602
X-RAY DIFFRACTIONr_scbond_it3.5872.9825697
X-RAY DIFFRACTIONr_scbond_other3.5872.9825698
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4694.2978290
X-RAY DIFFRACTIONr_long_range_B_refined6.89729.97112743
X-RAY DIFFRACTIONr_long_range_B_other6.84429.82412638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 395 -
Rwork0.286 7503 -
obs--96.31 %

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