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Yorodumi- PDB-3bfb: Crystal structure of a pheromone binding protein from Apis mellif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bfb | ||||||
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Title | Crystal structure of a pheromone binding protein from Apis mellifera in complex with the 9-keto-2(E)-decenoic acid | ||||||
Components | Pheromone-binding protein ASP1 | ||||||
Keywords | PHEROMONE BINDING PROTEIN / Honeybee / Apis mellifera / signal transduction / queen mandibular pheromone / PHEROMONE-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Apis mellifera (honey bee) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Pesenti, M.E. / Spinelli, S. / Bezirard, V. / Briand, L. / Pernollet, J.C. / Tegoni, M. / Cambillau, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural basis of the honey bee PBP pheromone and pH-induced conformational change 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 | 3bfb.cif.gz | 38.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bfb.ent.gz | 26.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/3bfb ftp://data.pdbj.org/pub/pdb/validation_reports/bf/3bfb | HTTPS FTP |
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-Related structure data
Related structure data | 3bfaC 3bfhC 3cabC 3cdnC 1r5r C: citing same article (ref.) S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 13194.789 Da / Num. of mol.: 1 / Fragment: UNP residues 26-144 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 | ||
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#2: Chemical | ChemComp-CL / | ||
#3: Chemical | ChemComp-9OD / ( | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 1.7M ammonium sulfate, 0.1M sodium citrate, pH5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 8, 2007 / Details: cylindrical grazing incidence mirror |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→57.3 Å / Num. obs: 9124 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 43.67 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 2.15→2.27 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1273 / Rsym value: 0.492 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1R5R 1r5r Resolution: 2.15→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.783 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.199 / 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: 40.979 Å2
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Refine analyze | Luzzati coordinate error free: 0.199 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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