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Yorodumi- PDB-1jv4: Crystal structure of recombinant major mouse urinary protein (rmu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jv4 | ||||||
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Title | Crystal structure of recombinant major mouse urinary protein (rmup) at 1.75 A resolution | ||||||
Components | Major urinary protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / lipocalin recombinant beta barrel | ||||||
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 / negative regulation of lipid storage ...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 / negative regulation of lipid storage / heat generation / small molecule binding / locomotor rhythm / negative regulation of gluconeogenesis / mitochondrion organization / aerobic respiration / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Kuser, P.R. / Franzoni, L. / Ferrari, E. / Spisni, A. / Polikarpov, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: The X-ray structure of a recombinant major urinary protein at 1.75 A resolution. A comparative study of X-ray and NMR-derived structures. Authors: Kuser, P.R. / Franzoni, L. / Ferrari, E. / Spisni, A. / Polikarpov, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Crystallization and preliminary diffraction studies of a recombinant major urinary protein Authors: Kuser, P.R. / Krauchenco, S. / Fangel, A. / Polikarpov, I. #2: Journal: Eur.J.Biochem. / Year: 1999 Title: Solution Structure of a Recombinant Mouse Major Urinary Protein Authors: Luecke, C. / Franzoni, L. / Abbate, F. / Lohr, F. / Ferrari, E. / Sorbi, R.T. / Rueterjans, H. / Spisni, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jv4.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jv4.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 1jv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jv4_validation.pdf.gz | 384.1 KB | Display | wwPDB validaton report |
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Full document | 1jv4_full_validation.pdf.gz | 389 KB | Display | |
Data in XML | 1jv4_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1jv4_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jv4 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jv4 | HTTPS FTP |
-Related structure data
Related structure data | 1mupS 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: 18733.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: group 1 major urinary protein / Plasmid: pHIL-D2 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P11589 | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-TZL / | #4: Water | ChemComp-HOH / | Sequence details | RESIDUE 136 IS GLN IN RMUP. THERE IS NO MUTATION WITH RESPECT TO ALL MUP ISOFORMS DEPOSITED IN SWS. ...RESIDUE 136 IS GLN IN RMUP. THERE IS NO MUTATION WITH RESPECT TO ALL MUP ISOFORMS DEPOSITED IN SWS. THE RECOMBINAN | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % | ||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 60mM CdCl2 and sodium phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K | ||||||||||||||||||
Crystal grow | *PLUS Temperature: 291 K | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.39 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 30, 1998 / Details: mirror |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.39 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→14 Å / Num. all: 54995 / Num. obs: 38851 / % possible obs: 87 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 2.46 / % possible all: 84.3 |
Reflection | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 14 Å / % possible obs: 86.4 % / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 89.6 % / Rmerge(I) obs: 0.299 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1mup.pdb Resolution: 1.75→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.75→14 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.206 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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