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Yorodumi- PDB-6z4k: A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z4k | ||||||
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Title | A4V mutant of human SOD1 bound with benzyl benzoisoselenazolone derivative 6 in P21 space group | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / SOD1 / ebselen / Motor neuron disease | ||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / retrograde axonal transport / relaxation of vascular associated smooth muscle / response to superoxide / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / myeloid cell homeostasis / regulation of GTPase activity / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / neuronal action potential / response to axon injury / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / reactive oxygen species metabolic process / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / positive regulation of cytokine production / determination of adult lifespan / locomotory behavior / sensory perception of sound / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / negative regulation of inflammatory response / regulation of blood pressure / small GTPase binding / peroxisome / Platelet degranulation / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / intracellular iron ion homeostasis / response to ethanol / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / positive regulation of apoptotic process / response to xenobiotic stimulus / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Amporndanai, K. / Hasnain, S.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Ebiomedicine / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z4k.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z4k.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6z4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z4k_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6z4k_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6z4k_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 6z4k_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/6z4k ftp://data.pdbj.org/pub/pdb/validation_reports/z4/6z4k | HTTPS FTP |
-Related structure data
Related structure data | 6z3vC 6z4gC 6z4hC 6z4iC 6z4jC 6z4lC 6z4mC 6z4oC 1uxmS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain: (Details: Chains AAA BBB) |
-Components
#1: Protein | Mass: 15855.613 Da / Num. of mol.: 2 / Mutation: A4V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pET303C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00441, superoxide dismutase #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | Y | |
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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: 2.02 Å3/Da / Density % sol: 39.02 % |
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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, 2.7M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 14, 2019 / Details: mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→34.33 Å / Num. obs: 44385 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.029 / Rrim(I) all: 0.042 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 3 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2224 / CC1/2: 0.609 / Rpim(I) all: 0.524 / Rrim(I) all: 0.769 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UXM Resolution: 1.45→34.33 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.707 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.081 / ESU R Free: 0.076 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: 20.308 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→34.33 Å
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Refine LS restraints |
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LS refinement shell |
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