+Open data
-Basic information
Entry | Database: PDB / ID: 3u5s | ||||||
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Title | Selenium Substituted Human Augmenter of Liver Regeneration | ||||||
Components | FAD-linked sulfhydryl oxidase ALR | ||||||
Keywords | OXIDOREDUCTASE / Flavin / Liver / selenium NMR / selenocysteine / selenoproteins / augmenter of liver regeneration | ||||||
Function / homology | Function and homology information flavin-dependent sulfhydryl oxidase activity / thiol oxidase / cellular response to toxic substance / negative regulation of natural killer cell mediated cytotoxicity / Mitochondrial protein import / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration ...flavin-dependent sulfhydryl oxidase activity / thiol oxidase / cellular response to toxic substance / negative regulation of natural killer cell mediated cytotoxicity / Mitochondrial protein import / positive regulation of DNA biosynthetic process / protein-disulfide reductase activity / cellular response to actinomycin D / liver development / liver regeneration / growth factor activity / mitochondrial intermembrane space / cellular response to tumor necrosis factor / flavin adenine dinucleotide binding / cellular response to lipopolysaccharide / negative regulation of apoptotic process / mitochondrion / extracellular space / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Dong, M. / Bahnson, B.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: (77)Se enrichment of proteins expands the biological NMR toolbox. Authors: Schaefer, S.A. / Dong, M. / Rubenstein, R.P. / Wilkie, W.A. / Bahnson, B.J. / Thorpe, C. / Rozovsky, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u5s.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u5s.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 3u5s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/3u5s ftp://data.pdbj.org/pub/pdb/validation_reports/u5/3u5s | HTTPS FTP |
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-Related structure data
Related structure data | 3mbgS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15454.029 Da / Num. of mol.: 1 / Mutation: C154A, C165A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GFER, ALR, HERV1, HPO / Production host: Escherichia coli (E. coli) / References: UniProt: P55789, thiol oxidase |
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#2: Chemical | ChemComp-FAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.76 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 7, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 16472 / Num. obs: 15561 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2 % / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 2.43 / Num. unique all: 723 / % possible all: 36.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MBG Resolution: 1.5→21.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.503 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R Free: 0.113 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.687 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→21.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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