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- PDB-3ix4: LasR-TP1 complex -

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Basic information

Entry
Database: PDB / ID: 3ix4
TitleLasR-TP1 complex
ComponentsTranscriptional activator protein lasR
KeywordsTRANSCRIPTION / Quorum sensing / triphenyl mimic / Activator / DNA-binding / Transcription regulation
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-TX1 / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZou, Y. / Nair, S.K.
CitationJournal: Chem.Biol. / Year: 2009
Title: Molecular basis for the recognition of structurally distinct autoinducer mimics by the Pseudomonas aeruginosa LasR quorum-sensing signaling receptor.
Authors: Zou, Y. / Nair, S.K.
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)159,14016
Polymers154,5918
Non-polymers4,5498
Water26,9681497
1
A: Transcriptional activator protein lasR
C: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7854
Polymers38,6482
Non-polymers1,1372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-17 kcal/mol
Surface area15090 Å2
MethodPISA
2
B: Transcriptional activator protein lasR
hetero molecules

E: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7854
Polymers38,6482
Non-polymers1,1372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_644-x+1,y-1/2,-z-11
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area15330 Å2
MethodPISA
3
D: Transcriptional activator protein lasR
G: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7854
Polymers38,6482
Non-polymers1,1372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-18 kcal/mol
Surface area15120 Å2
MethodPISA
4
F: Transcriptional activator protein lasR
hetero molecules

H: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7854
Polymers38,6482
Non-polymers1,1372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area2060 Å2
ΔGint-19 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.196, 84.546, 156.385
Angle α, β, γ (deg.)90.00, 95.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transcriptional activator protein lasR


Mass: 19323.857 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: lasR, PA1430 / Production host: Escherichia coli (E. coli) / References: UniProt: P25084
#2: Chemical
ChemComp-TX1 / 2,4-dibromo-6-({[(2-nitrophenyl)carbonyl]amino}methyl)phenyl 2-chlorobenzoate


Mass: 568.599 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H13Br2ClN2O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1497 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 276 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 16% PEG 4000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 276K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 348440 / Num. obs: 127357 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.054 / Net I/σ(I): 19.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Num. unique all: 11889 / Rsym value: 0.192 / % possible all: 91.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IX3

3ix3


Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.976 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24675 6404 5 %RANDOM
Rwork0.19887 ---
obs0.20126 120893 97.96 %-
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: 22.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å20.38 Å2
2--1.65 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10499 0 248 1497 12244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02211036
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0921.9814956
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80951322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55523.738511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.786151751
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7871564
X-RAY DIFFRACTIONr_chiral_restr0.0850.21535
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028620
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.25675
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.27559
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2171
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.2101
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5821.56819
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.992210480
X-RAY DIFFRACTIONr_scbond_it1.45335063
X-RAY DIFFRACTIONr_scangle_it2.2164.54476
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 430 -
Rwork0.232 8212 -
obs--90.8 %

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