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- PDB-3jpu: LasR-TP4 complex -

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Basic information

Entry
Database: PDB / ID: 3jpu
TitleLasR-TP4 complex
ComponentsTranscriptional activator protein lasR
KeywordsTRANSCRIPTION / Quorum sensing / triphenyl mimic / Activator / DNA-binding / Transcription regulation
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-TY4 / Transcriptional activator protein LasR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,25710
Polymers96,6195
Non-polymers2,6385
Water1,49583
1
A: Transcriptional activator protein lasR
hetero molecules

A: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7034
Polymers38,6482
Non-polymers1,0552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1810 Å2
ΔGint-13 kcal/mol
Surface area15340 Å2
MethodPISA
2
B: Transcriptional activator protein lasR
C: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7034
Polymers38,6482
Non-polymers1,0552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area15060 Å2
MethodPISA
3
D: Transcriptional activator protein lasR
E: Transcriptional activator protein lasR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7034
Polymers38,6482
Non-polymers1,0552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area15450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.148, 82.428, 90.493
Angle α, β, γ (deg.)90.00, 126.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transcriptional activator protein lasR


Mass: 19323.857 Da / Num. of mol.: 5
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-TY4 / 4-bromo-2-({[(2-chlorophenyl)carbonyl]amino}methyl)-6-methylphenyl 2,4-dichlorobenzoate


Mass: 527.622 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C22H15BrCl3NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.39 Å3/Da / Density % sol: 48.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 8000, 0.1 M ammonium sulfate, 0.05 M MES, 0.003 M DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 39050 / % possible obs: 96.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rsym value: 0.046 / Net I/σ(I): 23.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3226 / Rsym value: 0.365 / % possible all: 80.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0056refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IX3

3ix3


Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 19.758 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28061 1966 5 %RANDOM
Rwork0.22471 ---
obs0.22745 37071 96.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.848 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å23.4 Å2
2---0.12 Å20 Å2
3---3.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6358 0 150 83 6591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226683
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.989062
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19923.648307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.008151053
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0341540
X-RAY DIFFRACTIONr_chiral_restr0.1130.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215215
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_it0.6371.54005
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.16126355
X-RAY DIFFRACTIONr_scbond_it2.17332678
X-RAY DIFFRACTIONr_scangle_it3.2754.52707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 121 -
Rwork0.272 2143 -
obs--76.2 %
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)
19.7272-1.7033-5.17222.91930.16757.3256-0.4410.64810.6169-0.29660.3442-0.14820.524-0.32550.09680.0826-0.0882-0.00720.12240.04740.076-18.954-39.624224.6037
23.28250.72990.10845.57920.49473.3149-0.10680.30430.1702-0.0123-0.2941-0.4509-0.20030.21810.40090.0532-0.022-0.04760.15550.12050.1366-44.9109-35.4272-5.6463
34.2850.42220.33975.4283-0.13012.51110.0812-0.2924-0.19261.0631-0.20850.54830.2684-0.10040.12730.3174-0.05260.12490.0735-0.01290.0787-62.7619-53.65036.7341
47.770.4445-0.94664.6141-0.52473.2852-0.340.4645-1.272-0.3138-0.0312-0.08850.4966-0.29110.37130.14870.00410.07860.1058-0.0750.2904-73.9374-15.654121.146
56.91150.828-1.76314.0531-0.89692.6455-0.0835-1.0192-0.83460.4447-0.1139-0.6918-0.12140.73410.19730.18120.0318-0.08180.39380.18060.2892-47.4069-7.935927.6368
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 166
2X-RAY DIFFRACTION2B6 - 166
3X-RAY DIFFRACTION3C6 - 166
4X-RAY DIFFRACTION4D6 - 166
5X-RAY DIFFRACTION5E6 - 166

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