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Yorodumi- PDB-1znl: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1znl | |||||||||
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Title | Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex | |||||||||
Components | Major Urinary Protein | |||||||||
Keywords | TRANSPORT PROTEIN / lIPOCALIN / BETA-BARREL / DECAN-1-OL | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Malham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2005 Title: Strong Solute-Solute Dispersive Interactions in a Protein-Ligand Complex. Authors: Malham, R. / Johnstone, S. / Bingham, R.J. / Barratt, E. / Phillips, S.E. / Laughton, C.A. / Homans, S.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1znl.cif.gz | 53.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1znl.ent.gz | 36.4 KB | Display | PDB format |
PDBx/mmJSON format | 1znl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1znl_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
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Full document | 1znl_full_validation.pdf.gz | 450 KB | Display | |
Data in XML | 1znl_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 1znl_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/1znl ftp://data.pdbj.org/pub/pdb/validation_reports/zn/1znl | HTTPS FTP |
-Related structure data
Related structure data | 1zndC 1zneC 1zngC 1znhC 1znkC 1qy0S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 20139.400 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: MUP1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P11589 | ||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-DE1 / | #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: 2.75 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9 Details: CADMIUM CHLORIDE, MALATE, HCL, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38 Å / Num. all: 23022 / Num. obs: 23022 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 17 Å2 / Rsym value: 0.083 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3314 / Rsym value: 0.236 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QY0 Resolution: 1.7→38 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.76 Å / Rfactor Rfree error: 0.02
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