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- PDB-6z4h: A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6z4h | ||||||
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Title | A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 2 in P21 space group | ||||||
![]() | Superoxide dismutase [Cu-Zn] | ||||||
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Function / homology | ![]() action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Amporndanai, K. / Hasnain, S.S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Novel Selenium-based compounds with therapeutic potential for SOD1-linked amyotrophic lateral sclerosis. Authors: Amporndanai, K. / Rogers, M. / Watanabe, S. / Yamanaka, K. / O'Neill, P.M. / Hasnain, S.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6z3vC ![]() 6z4gC ![]() 6z4iC ![]() 6z4jC ![]() 6z4kC ![]() 6z4lC ![]() 6z4mC ![]() 6z4oC ![]() 1uxmS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
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Components
#1: Protein | Mass: 15855.613 Da / Num. of mol.: 2 / Mutation: A4V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ![]() #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: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow![]() | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 100mM NaOAc pH 4.7, 150mM NaCl, 2.6M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 29, 2020 |
Radiation | Monochromator: Single bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→39.84 Å / Num. obs: 18560 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 26.659 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.063 / Rrim(I) all: 0.091 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1259 / CC1/2: 0.538 / Rpim(I) all: 0.333 / Rrim(I) all: 0.48 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1UXM Resolution: 1.95→39.836 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.704 / SU ML: 0.134 / Cross valid method: FREE R-VALUE / ESU R: 0.233 / ESU R Free: 0.175 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.501 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→39.836 Å
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Refine LS restraints |
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LS refinement shell |
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