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Yorodumi- PDB-3d73: Crystal structure of a pheromone binding protein mutant D35A, fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d73 | ||||||
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Title | Crystal structure of a pheromone binding protein mutant D35A, from Apis mellifera, at pH 7.0 | ||||||
Components | Pheromone-binding protein ASP1 | ||||||
Keywords | Pheromone Binding Protein / Honey bee / Apis mellifera / signal transduction / queen mandibular protein / pH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Apis mellifera (honey bee) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Queen bee pheromone binding protein pH-induced domain swapping favors pheromone release Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Campanacci, V. / Tegoni, M. / Cambillau, C. #1: Journal: To be Published Title: The pH Driven Domain-swapping Dimerization of Queen Bee ASP1 Favours Pheromone Release Authors: Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d73.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d73.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 3d73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d73 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d73 | HTTPS FTP |
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-Related structure data
Related structure data | 3cyzC 3cz0C 3cz1C 3cz2C 3d74C 3d75C 3d76C 3d77C 3d78C 2h8vS 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13150.778 Da / Num. of mol.: 2 / Fragment: UNP residues 26-144 / Mutation: D35A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apis mellifera (honey bee) / Plasmid: pHIL-D2 / Production host: Pichia pastoris (fungus) / References: UniProt: Q9U9J6 #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: 2.03 Å3/Da / Density % sol: 39.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.1M ammonium sulfate, 0.2M di-ammonium phosphate, 20mM di-sodium phosphate, pH7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 14, 2008 / Details: polar mirror |
Radiation | Monochromator: Osmic vacuum / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→30.43 Å / Num. all: 14418 / Num. obs: 14418 / % possible obs: 97.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 21.84 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 2.01→2.12 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 6.4 / Num. unique all: 10192 / Rsym value: 0.254 / % possible all: 82.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2H8V Resolution: 2.03→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.978 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.183 / 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: 27.559 Å2
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Refine analyze | Luzzati coordinate error free: 0.183 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.025→2.077 Å / Total num. of bins used: 20
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