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- PDB-6d6a: The structure of ligand binding domain of LasR in complex with TP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6d6a | ||||||
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Title | The structure of ligand binding domain of LasR in complex with TP-1 homolog, compound 10 | ||||||
![]() | Transcriptional activator protein LasR | ||||||
![]() | signaling protein/agonist / LuxR receptor / signaling protein-agonist complex | ||||||
Function / homology | ![]() 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 / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Dong, S.H. / Nair, S.K. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 280.8 KB | Display | ![]() |
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PDB format | ![]() | 231.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6d6bC ![]() 6d6cC ![]() 6d6dC ![]() 6d6lC ![]() 6d6mC ![]() 6d6nC ![]() 6d6oC ![]() 6d6pC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19008.469 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lasR, PA1430 / Production host: ![]() ![]() #2: Chemical | ChemComp-FXD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 80 K / Ambient temp details: liquid nitrogen air flow |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 9, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 102583 / % possible obs: 97.56 % / Redundancy: 3.9 % / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.9→2 Å |
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Processing
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Refinement | Resolution: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.844 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→38.86 Å
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Refine LS restraints |
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