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Yorodumi- PDB-1g85: CRYSTAL STRUCTURE OF BOVINE ODORANT BINDING PROTEIN COMPLEXED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g85 | ||||||
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Title | CRYSTAL STRUCTURE OF BOVINE ODORANT BINDING PROTEIN COMPLEXED WITH IS NATURAL LIGAND | ||||||
Components | ODORANT-BINDING PROTEIN | ||||||
Keywords | SIGNALING PROTEIN / lipocalin / swapping domain / homodimer | ||||||
Function / homology | Function and homology information odorant binding / response to stimulus / small molecule binding / sensory perception of smell / extracellular space Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Vincent, F. / Spinelli, S. / Cambillau, C. / Tegoni, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 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. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Domain swapping creates a third putative combining site in bovine odorant binding protein dimer. Authors: Tegoni, M. / Spinelli, S. / Cambillau, C. / Spinelli, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g85.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g85.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 1g85.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g85 ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g85 | HTTPS FTP |
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-Related structure data
Related structure data | 1hn2C 1pboS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18456.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P07435 #2: Chemical | ChemComp-3OL / ( #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: 2.09 Å3/Da / Density % sol: 41.21 % |
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Crystal grow | Temperature: 277 K / Method: microdialysis / pH: 5.7 Details: 38% ethanol, 25mM sodium citrate, pH 5.7, MICRODIALYSIS, temperature 4K, temperature 277K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 2000 / Details: osmic mirrors |
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→55 Å / Num. all: 237362 / Num. obs: 107952 / % possible obs: 45 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 35.94 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.8→55 Å / Redundancy: 4 % / Rmerge(I) obs: 0.23 / Num. unique all: 27620 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1PBO Resolution: 1.8→25.3 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 42.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.02
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