+Open data
-Basic information
Entry | Database: PDB / ID: 8j8e | ||||||
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Title | Human serum albumin-palladium(II) agent complex | ||||||
Components | Serum albumin | ||||||
Keywords | HORMONE / Complex | ||||||
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 / small molecule 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: 2.5 Å | ||||||
Authors | Zhang, Z.L. / Zhang, J.Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of human serum albumin palladium(II) agent complex Authors: Zhang, Z.L. / Zhang, J.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j8e.cif.gz | 240.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j8e.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 8j8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/8j8e ftp://data.pdbj.org/pub/pdb/validation_reports/j8/8j8e | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02768 #2: Chemical | ChemComp-PLM / #3: Chemical | Mass: 389.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N4PdS / Feature type: SUBJECT OF INVESTIGATION #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.42 Å3/Da / Density % sol: 49.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 30% PEG 3350, 0.05M PB 7.0, 5% G, 5% DMSO |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 5, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→91.96 Å / Num. obs: 42319 / % possible obs: 98.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.177 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.177 / Num. unique obs: 3143 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→91.96 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.86 / SU B: 18.748 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R: 1.136 / ESU R Free: 0.39 / 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: 46.276 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→91.96 Å
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