+Open data
-Basic information
Entry | Database: PDB / ID: 1a3y | ||||||
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Title | ODORANT BINDING PROTEIN FROM NASAL MUCOSA OF PIG | ||||||
Components | ODORANT BINDING PROTEIN | ||||||
Keywords | LIPOCALIN / OLFACTION | ||||||
Function / homology | Function and homology information odorant binding / small molecule binding / sensory perception of smell / extracellular space Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Spinelli, S. / Cambillau, C. / Tegoni, M. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: The structure of the monomeric porcine odorant binding protein sheds light on the domain swapping mechanism. Authors: Spinelli, S. / Ramoni, R. / Grolli, S. / Bonicel, J. / Cambillau, C. / Tegoni, M. #1: Journal: Chem.Senses / Year: 1995 Title: Affinities of Nutty and Green-Smelling Pyrazines and Thiazoles to Odorant-Binding Proteins, in Relation with Their Lipophilicity Authors: Herent, M.F. / Collin, S. / Pelosi, P. #2: Journal: Chem.Senses / Year: 1993 Title: Binding of Selected Odorant to Bovine and Porcine Odorant-Binding Proteins Authors: Monte, M.D. / Centini, M. / Anselmi, C. / Pelosi, P. #3: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 1991 Title: Purification and Characterization of Two Odorant-Binding Proteins from Nasal Tissue of Rabbit and Pig Authors: Dal Monte, M. / Andreini, I. / Revoltella, R. / Pelosi, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a3y.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a3y.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 1a3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a3y_validation.pdf.gz | 393.2 KB | Display | wwPDB validaton report |
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Full document | 1a3y_full_validation.pdf.gz | 396.5 KB | Display | |
Data in XML | 1a3y_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1a3y_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/1a3y ftp://data.pdbj.org/pub/pdb/validation_reports/a3/1a3y | HTTPS FTP |
-Related structure data
Related structure data | 1obpS 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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Unit cell |
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-Components
#1: Protein | Mass: 16769.480 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: NOSE / Tissue: OLFACTORY EPITHELIUM / References: UniProt: P81245 #2: 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: 2.3 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. obs: 11000 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rsym value: 0.051 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.265 / % possible all: 99 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.265 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OBP Resolution: 2.25→25 Å / Rfactor Rfree error: 0.0002 / Data cutoff high absF: 10000000 / Data cutoff low absF: 100 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.25→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.37 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 7
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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