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Yorodumi- PDB-1gnj: HUMAN SERUM ALBUMIN COMPLEXED WITH cis-5,8,11,14-EICOSATETRAENOIC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gnj | ||||||
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Title | HUMAN SERUM ALBUMIN COMPLEXED WITH cis-5,8,11,14-EICOSATETRAENOIC ACID (ARACHIDONIC ACID) | ||||||
Components | SERUM ALBUMIN | ||||||
Keywords | PLASMA PROTEIN / METAL-BINDING / LIPID-BINDING / GLYCOPROTEIN | ||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / pyridoxal phosphate binding / Platelet degranulation / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Petitpas, I. / Gruene, T. / Bhattacharya, A.A. / Curry, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal Structures of Human Serum Albumin Complexed with Monounsaturated and Polyunsaturated Fatty Acids. Authors: Petitpas, I. / Gruene, T. / Bhattacharya, A.A. / Curry, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gnj.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gnj.ent.gz | 100.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gnj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/1gnj ftp://data.pdbj.org/pub/pdb/validation_reports/gn/1gnj | HTTPS FTP |
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-Related structure data
Related structure data | 1gniC 1bj5S 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: 66571.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02768 | ||||
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#2: Chemical | ChemComp-ACD / #3: Water | ChemComp-HOH / | Compound details | FUNCTION:SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE PRESSURE OF BLOOD. IT BINDS TO ...FUNCTION:SERUM ALBUMIN, REGULATES THE COLLOIDAL OSMOTIC PRESSURE PRESSURE OF BLOOD. IT BINDS TO WATER, CA++, NA+, K+, FATTY ACIDS HORMONES, BILIRUBIN AND DRUGS | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.00 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9102 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: TRIANGULAR MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9102 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.6 Å / Num. obs: 20374 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 57.8 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 2.3 / % possible all: 76 |
Reflection shell | *PLUS % possible obs: 76 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJ5 Resolution: 2.6→29.62 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1638392.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED RESIDUES ASP 1, ALA 2 AND LEU 585 ARE DISORDERED AND HAVE NOT BEEN INCLUDED IN THE MODEL.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.4052 Å2 / ksol: 0.285785 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.314 |