+Open data
-Basic information
Entry | Database: PDB / ID: 3ix8 | ||||||
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Title | LasR-TP3 complex | ||||||
Components | Transcriptional activator protein lasRActivator (genetics) | ||||||
Keywords | TRANSCRIPTION / 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 | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zou, Y. / Nair, S.K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ix8.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ix8.ent.gz | 120.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ix8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ix8 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ix8 | HTTPS FTP |
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-Related structure data
Related structure data | 3ix4C 3jpuC 3ix3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19323.857 Da / Num. of mol.: 4 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-TX3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.89 % |
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Crystal grow | Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 16% PEG 4000, 0.04 M HEPES, 0.08 M calcium acetate, 0.003 M DTT, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 276K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 62337 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rsym value: 0.037 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 5.3 / Num. unique all: 5650 / Rsym value: 0.182 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3IX3 Resolution: 1.8→25 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.04 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.152 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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