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- PDB-3bjh: Soft-SAD crystal structure of a pheromone binding protein from th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bjh | |||||||||
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Title | Soft-SAD crystal structure of a pheromone binding protein from the honeybee Apis mellifera L. | |||||||||
![]() | Pheromone-binding protein ASP1 | |||||||||
![]() | PHEROMONE BINDING PROTEIN / Honeybee / Apis mellifera / signal transduction | |||||||||
Function / homology | ![]() dibutyl phthalate binding / olfactory behavior / odorant binding / sensory perception of smell / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lartigue, A. / Gruez, A. / Briand, L. / Blon, F. / Bezirard, V. / Walsh, M. / Pernollet, J.C. / Tegoni, M. / Cambillau, C. | |||||||||
![]() | ![]() Title: Sulfur single-wavelength anomalous diffraction crystal structure of a pheromone-binding protein from the honeybee Apis mellifera L. Authors: Lartigue, A. / Gruez, A. / Briand, L. / Blon, F. / Walsh, M. / Pernollet, J.C. / Tegoni, M. / Cambillau, C. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 36.1 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 429.5 KB | Display | ![]() |
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Full document | ![]() | 429.4 KB | Display | |
Data in XML | ![]() | 4.9 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NBB / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5M ammonium sulfate, 0.15M sodium citrate, pH5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 2002 / Details: mirrors |
Radiation | Monochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.8 Å / Num. obs: 22274 / % possible obs: 99.6 % / Observed criterion σ(F): 5.4 / Redundancy: 5.2 % / Rmerge(I) obs: 0.062 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 32.369 Å2
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Refine analyze | Luzzati coordinate error free: 0.08 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 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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