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Open data
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Basic information
Entry | Database: PDB / ID: 1hn2 | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE OBP COMPLEXED WITH AMINOANTHRACENE | ||||||
![]() | ODORANT-BINDING PROTEIN | ||||||
![]() | PROTEIN BINDING / olfaction / odorant binding protein / aminoanthracene | ||||||
Function / homology | ![]() odorant binding / response to stimulus / small molecule binding / sensory perception of smell / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Vincent, F. / Spinelli, S. / Tegoni, M. / Cambillau, C. | ||||||
![]() | ![]() Title: The insect attractant 1-octen-3-ol is the natural ligand of bovine odorant-binding protein. Authors: Ramoni, R. / Vincent, F. / Grolli, S. / Conti, V. / Malosse, C. / Boyer, F.D. / Nagnan-Le Meillour, P. / Spinelli, S. / Cambillau, C. / Tegoni, M. | ||||||
History |
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Remark 600 | heterogen The Native Bovine OBP has a natural ligand Octene-3-ol (PDB ID 1G85). In this experiment, ...heterogen The Native Bovine OBP has a natural ligand Octene-3-ol (PDB ID 1G85). In this experiment, the native Bovine OBP was soaked with 2mM Aminoanthracene, which removed all of the natural ligand in cavity A (giving all Aminoantracene atoms occupancy 1.0) but left 40% of the natural ligand in cavity B. The occupancy of aminoanthracene atoms in cavity B was 0.60 because of the presence of octene-3-ol, with the R and S enantiomers each having occupancies of 0.20. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 60.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.3 KB | Display | ![]() |
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Full document | ![]() | 480.2 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g85C ![]() 1obpS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 18528.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-3OL / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.72 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5.7 Details: dialysys against 38% ethanol in 25 mM sodium Citrate at 4 degrees, pH 5.7 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5.4 / Method: microdialysis | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 28, 2000 |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→17 Å / Num. obs: 26203 / % possible obs: 92 % / Redundancy: 2.8 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 5.2 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.8→1.89 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.44 / % possible all: 85.4 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 18 Å / % possible obs: 92 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.84 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OBP Resolution: 1.8→9.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1113369.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 73.09 Å2 / ksol: 0.362 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→9.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 15530 / % reflection Rfree: 4.8 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.237 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.325 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.289 |