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Yorodumi- PDB-1t14: Crystal structure of LUSH from Drosophila melanogaster: apo protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t14 | ||||||
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Title | Crystal structure of LUSH from Drosophila melanogaster: apo protein | ||||||
Components | lush | ||||||
Keywords | TRANSPORT PROTEIN / LUSH / ALCOHOL / ODORANT BINDING | ||||||
Function / homology | Function and homology information diphenyl phthalate binding / courtship behavior / dibutyl phthalate binding / response to pheromone / pheromone binding / olfactory behavior / odorant binding / sensory perception of smell / response to ethanol / extracellular region Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Kruse, S.W. / Jones, D.N.M. | ||||||
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 | 1t14.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t14.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 1t14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/1t14 ftp://data.pdbj.org/pub/pdb/validation_reports/t1/1t14 | HTTPS FTP |
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-Related structure data
Related structure data | 3b6xC 3b7aC 3b86C 3b87C 3b88C 1oofS 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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1 |
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2 |
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Unit cell |
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Details | There are two biological units in the assymetric unit, chains A and B |
-Components
#1: Protein | Mass: 14215.508 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: lush / Plasmid: pET13a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O02372 #2: Chemical | #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: 2.16 Å3/Da / Density % sol: 36.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 31, 2003 / Details: OSMIC BLUE OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. all: 20245 / Num. obs: 19577 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.86→1.93 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 4.6 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1OOF Resolution: 1.86→15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.794 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.959 Å / Total num. of bins used: 10 /
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