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Yorodumi- PDB-8ew7: Human Serum Albumin with Cobalt (II) and Myristic Acid - crystal 2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ew7 | |||||||||
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Title | Human Serum Albumin with Cobalt (II) and Myristic Acid - crystal 2 | |||||||||
Components | Serum albumin | |||||||||
Keywords | TRANSPORT PROTEIN / serum albumin / complex with cobalt / albumin with fatty acid / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID / Center for Structural Biology of Infectious Diseases / CSBID | |||||||||
Function / homology | Function and homology information exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / cellular response to calcium ion starvation / 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 / molecular replacement / Resolution: 3.3 Å | |||||||||
Authors | Gucwa, M. / Cooper, D.R. / Stewart, A.J. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID) / Center for Structural Biology of Infectious Diseases (CSBID) | |||||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2023 Title: Structural and biochemical characterisation of Co2+-binding sites on serum albumins and their interplay with fatty acids Authors: Wu, D. / Gucwa, M. / Czub, M.P. / Cooper, D.R. / Shabalin, I.G. / Fritzen, R. / Arya, S. / Schwarz-Linek, U. / Blindauer, C.A. / Minor, W. / Stewart, A.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ew7.cif.gz | 132.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ew7.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 8ew7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ew7_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8ew7_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8ew7_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 8ew7_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ew/8ew7 ftp://data.pdbj.org/pub/pdb/validation_reports/ew/8ew7 | HTTPS FTP |
-Related structure data
Related structure data | 7mblC 8ew4C 8ey5C 6wuwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-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 natural source / Source: (natural) Homo sapiens (human) / Tissue: Blood / References: UniProt: P02768 | ||||||||
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#2: Chemical | ChemComp-CO / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44 % / Description: Rectangular prisms |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 200 nL 18% PEG3350, 50 mM Tris, pH 7.4 + 200 nL 50 mg/mL albumin, 50% saturated myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. Addition of 40% PEG3350, 50 mM Tris, 20 mM cobalt ...Details: 200 nL 18% PEG3350, 50 mM Tris, pH 7.4 + 200 nL 50 mg/mL albumin, 50% saturated myristic acid, 50 mM sodium chloride, 25 mM Tris, pH 7.4. Addition of 40% PEG3350, 50 mM Tris, 20 mM cobalt (II) chloride 6 hours prior to harvesting. |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Nitrogen stream / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.60311 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2022 / Details: Sagittal focusing | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.60311 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.3→40 Å / Num. obs: 9385 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Rrim(I) all: 0.134 / Χ2: 0.907 / Net I/σ(I): 5 / Num. measured all: 61539 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6WUW Resolution: 3.3→37.28 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.832 / SU B: 32.636 / SU ML: 0.531 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.699 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 118.2 Å2 / Biso mean: 44.521 Å2 / Biso min: 0.5 Å2
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Refinement step | Cycle: final / Resolution: 3.3→37.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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