+Open data
-Basic information
Entry | Database: PDB / ID: 4k2c | ||||||
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Title | HSA Ligand Free | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / Heart Shape | ||||||
Function / homology | Function and homology information cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / HDL remodeling / enterobactin binding / Heme biosynthesis / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / antioxidant activity / Aspirin ADME / 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: 3.23 Å | ||||||
Authors | Wang, Y. / Luo, Z. / Shi, X. / Huang, M. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2013 Title: Structural mechanism of ring-opening reaction of glucose by human serum albumin. Authors: Wang, Y. / Yu, H. / Shi, X. / Luo, Z. / Lin, D. / Huang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4k2c.cif.gz | 448.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4k2c.ent.gz | 388.2 KB | Display | PDB format |
PDBx/mmJSON format | 4k2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/4k2c ftp://data.pdbj.org/pub/pdb/validation_reports/k2/4k2c | HTTPS FTP |
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-Related 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 genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 Production host: Pichia pastoris (fungus) / References: UniProt: P02768 |
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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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7 Details: 25-30% PEG 3350, pH 7, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.04 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 3.03→50 Å / Num. obs: 18979 |
Reflection shell | Highest resolution: 3.03 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→47.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 83.872 / SU ML: 0.548 / Cross valid method: THROUGHOUT / ESU R Free: 0.763 / 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: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 105.526 Å2
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Refinement step | Cycle: LAST / Resolution: 3.23→47.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.23→3.314 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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