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Yorodumi- PDB-1i05: CRYSTAL STRUCTURE OF MOUSE MAJOR URINARY PROTEIN (MUP-I) COMPLEXE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i05 | ||||||
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Title | CRYSTAL STRUCTURE OF MOUSE MAJOR URINARY PROTEIN (MUP-I) COMPLEXED WITH HYDROXY-METHYL-HEPTANONE | ||||||
Components | MAJOR URINARY PROTEIN I | ||||||
Keywords | TRANSPORT PROTEIN / lipocalin / beta-barrel / pheromone | ||||||
Function / homology | Function and homology information positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / energy reserve metabolic process / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation ...positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / energy reserve metabolic process / positive regulation of glucose metabolic process / insulin receptor activity / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cellular response to lipid / heat generation / small molecule binding / locomotor rhythm / negative regulation of lipid storage / negative regulation of gluconeogenesis / aerobic respiration / mitochondrion organization / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Timm, D.E. / Baker, L.J. / Mueller, H. / Zidek, L. / Novotny, M.V. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Structural Basis of Pheromone Binding to Mouse Major Urinary Protein (MUP-I) Authors: Timm, D.E. / Baker, L.J. / Mueller, H. / Zidek, L. / Novotny, M.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i05.cif.gz | 48.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i05.ent.gz | 33.1 KB | Display | PDB format |
PDBx/mmJSON format | 1i05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1i05_validation.pdf.gz | 440.3 KB | Display | wwPDB validaton report |
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Full document | 1i05_full_validation.pdf.gz | 441.2 KB | Display | |
Data in XML | 1i05_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 1i05_validation.cif.gz | 12.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/1i05 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/1i05 | HTTPS FTP |
-Related structure data
Related structure data | 1i04C 1i06C 1mupS 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: 20674.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: MUP-I / Production host: Escherichia coli (E. coli) / References: UniProt: P02762 | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-LTL / | #4: 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: 2.13 Å3/Da / Density % sol: 42.19 % | ||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 200 mM maleate/HCl, 100 mM cadmium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 23, 1999 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 12397 / Num. obs: 12397 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.329 / % possible all: 98.6 |
Reflection | *PLUS Num. measured all: 40377 |
Reflection shell | *PLUS % possible obs: 98.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MUP Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 2 / Rfactor Rfree: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |