+Open data
-Basic information
Entry | Database: PDB / ID: 5yxe | ||||||
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Title | Crystal Structure Analysis of feline serum albumin | ||||||
Components | Serum albumin | ||||||
Keywords | TRANSPORT PROTEIN / fatty acid binding / drug binding | ||||||
Function / homology | Function and homology information maintenance of mitochondrion location / enterobactin binding / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space ...maintenance of mitochondrion location / enterobactin binding / toxic substance binding / cellular response to starvation / fatty acid binding / pyridoxal phosphate binding / negative regulation of apoptotic process / protein-containing complex / DNA binding / extracellular space / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Felis catus (domestic cat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.40241519802 Å | ||||||
Authors | Kihira, K. / Yokomaku, K. / Akiyama, M. / Morita, Y. / Komatsu, T. | ||||||
Citation | Journal: J Mater Chem B. / Year: 2018 Title: Core-shell protein cluster comprising haemoglobin and recombinant feline serum albumin as an artificial O2 carrier for cats Authors: Yokomaku, K. / Akiyama, M. / Morita, Y. / Kihira, K. / Komatsu, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yxe.cif.gz | 123.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yxe.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 5yxe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yx/5yxe ftp://data.pdbj.org/pub/pdb/validation_reports/yx/5yxe | HTTPS FTP |
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-Related structure data
Related structure data | 3lu8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65938.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Felis catus (domestic cat) / Gene: ALB / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: P49064 |
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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: 2.36 Å3/Da / Density % sol: 47.98 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion Details: 47mg/mL FSA in 10mM Na Phosphate pH7.4, 35% PEG3350, 0.2M Na malonate pH4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→46.8 Å / Num. obs: 8375 / % possible obs: 96.97 % / Redundancy: 3.4 % / Biso Wilson estimate: 108.51377052 Å2 / CC1/2: 0.973 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 3.4→3.61 Å / Num. unique obs: 2486 / CC1/2: 0.617 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3LU8 Resolution: 3.40241519802→46.7954450011 Å / SU ML: 0.405194207028 / Cross valid method: FREE R-VALUE / σ(F): 1.3378403567 / Phase error: 40.357215519
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 115.072719198 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.40241519802→46.7954450011 Å
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Refine LS restraints |
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LS refinement shell |
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