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Yorodumi- PDB-3a73: Crystal Structure Analysis of Human serum albumin complexed with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a73 | ||||||
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Title | Crystal Structure Analysis of Human serum albumin complexed with delta 12-prostaglandin J2 | ||||||
Components | Serum albumin | ||||||
Keywords | LIPID BINDING PROTEIN / alpha-helical strcture / Cleavage on pair of basic residues / Disease mutation / Disulfide bond / Glycation / Glycoprotein / Lipid-binding / Metal-binding / Phosphoprotein / Secreted | ||||||
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: 2.19 Å | ||||||
Authors | Ito, S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Delta12-prostaglandin J2 as a product and ligand of human serum albumin: formation of an unusual covalent adduct at His146. Authors: Yamaguchi, S. / Aldini, G. / Ito, S. / Morishita, N. / Shibata, T. / Vistoli, G. / Carini, M. / Uchida, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a73.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a73.ent.gz | 198.4 KB | Display | PDB format |
PDBx/mmJSON format | 3a73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a7/3a73 ftp://data.pdbj.org/pub/pdb/validation_reports/a7/3a73 | HTTPS FTP |
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-Related structure data
Related structure data | 1bj5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 66571.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: serum / References: UniProt: P02768 #2: Chemical | ChemComp-MYR / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM phosphate buffer pH 6.5, 28-32% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→35.08 Å / Num. all: 68079 / Num. obs: 62497 / % possible obs: 92 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 4496 / Num. unique all: 5755 / Rsym value: 0.118 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BJ5 Resolution: 2.19→35 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.869 / SU B: 16.003 / SU ML: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.488 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.193→2.25 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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