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Yorodumi- PDB-3b7a: Complex of S52A Substituted Droposphila LUSH protein with Ethanol -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b7a | ||||||
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Title | Complex of S52A Substituted Droposphila LUSH protein with Ethanol | ||||||
Components | General odorant-binding protein lush | ||||||
Keywords | TRANSPORT PROTEIN / Odorant Binding Protein / Alochol Binding Protein / Behavior / Olfaction / Pheromone response / Pheromone-binding / Secreted / Sensory transduction / Transport | ||||||
Function / homology | Function and homology information diphenyl phthalate binding / courtship behavior / response to pheromone / dibutyl phthalate binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 3b7a.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b7a.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 3b7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b7a_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 3b7a_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 3b7a_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 3b7a_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/3b7a ftp://data.pdbj.org/pub/pdb/validation_reports/b7/3b7a | HTTPS FTP |
-Related structure data
Related structure data | 1t14C 3b6xC 3b86C 3b87C 3b88C 1oohS 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: 14199.508 Da / Num. of mol.: 2 / Mutation: S52A 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-EOH / | #3: Chemical | ChemComp-ACT / #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: 2.15 Å3/Da / Density % sol: 42.81 % |
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Crystal grow | Temperature: 295 K / pH: 4.6 Details: 25% PEG 4000, 100mM Sodium Acetate, 3:1 protein/well solution, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.12 Å |
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Detector | Type: NOIR-1 / Detector: CCD / Date: Jul 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→35.76 Å / Num. obs: 25896 / % possible obs: 98.9 % / Redundancy: 3.35 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.91 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.3 / % possible all: 99.8 |
-Phasing
Phasing MR | Rfactor: 0.34 / Cor.coef. Fo:Fc: 0.705
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OOH Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.762 / SU ML: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.28 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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