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- PDB-8a9q: Computational design of stable mammalian serum albumins for bacte... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a9q | |||||||||
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Title | Computational design of stable mammalian serum albumins for bacterial expression | |||||||||
![]() | Albumin | |||||||||
![]() | TRANSPORT PROTEIN / Complex with Warfarin | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Khersonsky, O. / Dym, O. / Fleishman, J.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Stable Mammalian Serum Albumins Designed for Bacterial Expression. Authors: Khersonsky, O. / Goldsmith, M. / Zaretsky, I. / Hamer-Rogotner, S. / Dym, O. / Unger, T. / Yona, M. / Fridmann-Sirkis, Y. / Fleishman, S.J. #1: ![]() Title: Stable mammalian serum albumins designed for bacterial expression Authors: Khersonsky, O. / Goldsmith, M. / Zaretsky, I. / Rogotner, S. / Dym, O. / Unger, T. / Yona, M. / Fleishman, S.J. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 236.6 KB | Display | ![]() |
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PDB format | ![]() | 187.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 43.4 KB | Display | |
Data in CIF | ![]() | 59.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hsc S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 66729.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Few designed mutations / Source: (gene. exp.) ![]() ![]() Gene: ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 Production host: ![]() ![]() #2: Chemical | ChemComp-MYR / #3: Chemical | #4: Chemical | ChemComp-DAO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.57 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: .05M NaCl, 10% PEG 4000 and 0.05 Tris pH=8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 20, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.02 Å / Num. obs: 74409 / % possible obs: 89.1 % / Redundancy: 1.5 % / Biso Wilson estimate: 41.82 Å2 / CC1/2: 0.945 / CC star: 0.986 / Rmerge(I) obs: 0.05816 / Rpim(I) all: 0.05186 / Rrim(I) all: 0.08224 / Net I/σ(I): 18.11 |
Reflection shell | Resolution: 2→2.071 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.2589 / Num. unique obs: 7010 / CC1/2: 0.86 / Rpim(I) all: 0.2589 / Rrim(I) all: 0.3661 / % possible all: 84.48 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6HSC ![]() 6hsc Resolution: 2→46.02 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 14.224 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.206 / 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: 39.111 Å2
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Refinement step | Cycle: 1 / Resolution: 2→46.02 Å
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