+Open data
-Basic information
Entry | Database: PDB / ID: 3b88 | ||||||
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Title | Complex of T57A Substituted Drosophila LUSH Protein with Ethanol | ||||||
Components | General odorant-binding protein lush | ||||||
Keywords | TRANSPORT PROTEIN / Odorant Binding Protein Alcohol Binding Protein / Behavior / Olfaction / Pheromone response / Pheromone-binding / Secreted / Sensory transduction / Transport | ||||||
Function / homology | Function and homology information diphenyl phthalate binding / dibutyl phthalate binding / courtship behavior / olfactory behavior / response to pheromone / pheromone binding / odorant binding / sensory perception of smell / response to ethanol / extracellular region Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Jones, D.N.M. / Thode, A.B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The role of multiple hydrogen-bonding groups in specific alcohol binding sites in proteins: insights from structural studies of LUSH. Authors: Thode, A.B. / Kruse, S.W. / Nix, J.C. / Jones, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b88.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b88.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 3b88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/3b88 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/3b88 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 14185.482 Da / Num. of mol.: 2 / Fragment: Chain A / Mutation: Threonine to Alanine Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: lush, Obp76a, Obp76c / Production host: Escherichia coli (E. coli) / References: UniProt: O02372 #2: Chemical | ChemComp-ACT / | #3: Chemical | #4: 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: 2.13 Å3/Da / Density % sol: 42.35 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.06 Å |
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Detector | Type: NOIR-1 / Detector: CCD / Date: Nov 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06 Å / Relative weight: 1 |
Reflection | Resolution: 2→36.85 Å / Num. obs: 16772 / % possible obs: 99.8 % / Redundancy: 6.88 % / Rmerge(I) obs: 0.068 / Χ2: 0.96 / Net I/σ(I): 15 / Scaling rejects: 873 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 6.75 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 5 / Num. measured all: 11157 / Num. unique all: 1650 / Χ2: 0.99 / % possible all: 99.6 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.85 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.35 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.189 / 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: 28.865 Å2
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Refinement step | Cycle: LAST / Resolution: 2→36.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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