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Yorodumi- PDB-3kfi: Major mouse urinary protein IV complexed with 2,5-dimethylpyrazine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kfi | ||||||
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Title | Major mouse urinary protein IV complexed with 2,5-dimethylpyrazine | ||||||
Components | Major urinary protein 4 | ||||||
Keywords | TRANSPORT PROTEIN / pheromone / major urinary protein / lipocalin / beta barrel / Disulfide bond / Pheromone-binding / Secreted / Transport | ||||||
Function / homology | Function and homology information positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / cellular response to lipid / 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 / heat generation ...positive regulation of lipid metabolic process / pheromone binding / negative regulation of lipid biosynthetic process / odorant binding / cellular response to lipid / 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 / 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 / molecular replacement / Resolution: 1.42 Å | ||||||
Authors | Perez-Miller, S. / Zou, Q. / Hurley, T.D. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: High resolution X-ray structures of mouse major urinary protein nasal isoform in complex with pheromones. Authors: Perez-Miller, S. / Zou, Q. / Novotny, M.V. / Hurley, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kfi.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kfi.ent.gz | 64.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kfi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kfi_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 3kfi_full_validation.pdf.gz | 437.7 KB | Display | |
Data in XML | 3kfi_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 3kfi_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/3kfi ftp://data.pdbj.org/pub/pdb/validation_reports/kf/3kfi | HTTPS FTP |
-Related structure data
Related structure data | 3kffC 3kfgC 3kfhC 1i06S C: citing same article (ref.) 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: 18846.436 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mup4 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11590 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-25R / | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
-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: 41.01 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 0.2-0.5 M calcium chloride dihydrate, 20% (w/v) polyethylene glycol 3350, pH 6, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 6, 2003 |
Radiation | Monochromator: OSMIC CONFOCAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→50 Å / Num. obs: 29102 / % possible obs: 95.1 % / Observed criterion σ(I): 0.2 / Redundancy: 2.9 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.42→1.47 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 2.4 / % possible all: 83.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MUP-I (PDB ENTRY 1I06) Resolution: 1.42→17.8 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: anisotropic individual / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.42→17.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.42→1.45 Å
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