+Open data
-Basic information
Entry | Database: PDB / ID: 1uxm | ||||||
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Title | A4V mutant of human SOD1 | ||||||
Components | SUPEROXIDE DISMUTASE [CU-ZN] | ||||||
Keywords | OXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL- BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION | ||||||
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 / relaxation of vascular associated smooth muscle / response to superoxide / retrograde axonal transport / 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 / relaxation of vascular associated smooth muscle / response to superoxide / retrograde axonal transport / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of protein kinase activity / regulation of T cell differentiation in thymus / retina homeostasis / superoxide anion generation / negative regulation of cholesterol biosynthetic process / auditory receptor cell stereocilium organization / hydrogen peroxide biosynthetic process / myeloid cell homeostasis / positive regulation of catalytic activity / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / superoxide dismutase / negative regulation of reproductive process / Detoxification of Reactive Oxygen Species / negative regulation of developmental process / transmission of nerve impulse / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / ovarian follicle development / positive regulation of phagocytosis / 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 / locomotory behavior / determination of adult lifespan / sensory perception of sound / response to hydrogen peroxide / placenta development / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / protein-folding chaperone binding / gene expression / response to heat / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / 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: 1.9 Å | ||||||
Authors | Hough, M.A. / Grossmann, J.G. / Antonyuk, S.V. / Strange, R.W. / Doucette, P.A. / Rodriguez, J.A. / Whitson, L.J. / Hart, P.J. / Hayward, L.J. / Valentine, J.S. / Hasnain, S.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Dimer Destabilization in Superoxide Dismutase May Result in Disease-Causing Properties: Structures of Motor Neuron Disease Mutants Authors: Hough, M.A. / Grossmann, J.G. / Antonyuk, S.V. / Strange, R.W. / Doucette, P.A. / Rodriguez, J.A. / Whitson, L.J. / Hart, P.J. / Hayward, L.J. / Valentine, J.S. / Hasnain, S.S. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA DA GA HA KA LA" IN EACH CHAIN ON ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA DA GA HA KA LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uxm.cif.gz | 364.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uxm.ent.gz | 297 KB | Display | PDB format |
PDBx/mmJSON format | 1uxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/1uxm ftp://data.pdbj.org/pub/pdb/validation_reports/ux/1uxm | HTTPS FTP |
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-Related structure data
Related structure data | 1uxlC 1hl5S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 15855.613 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): EG118 / Variant (production host): YEP351 / References: UniProt: P00441, superoxide dismutase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Water | ChemComp-HOH / | Compound details | DESTROYS RADICALS WHICH ARE NORMALLY PRODUCED WITHIN THE CELLS AND WHICH ARE TOXIC TO BIOLOGICAL ...DESTROYS RADICALS WHICH ARE NORMALLY PRODUCED WITHIN THE CELLS AND WHICH ARE TOXIC TO BIOLOGICAL | |
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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: 4.2 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: 0.2 M CA ACET, 15% PEG 2000, 0.1 M TRIS PH 8.0 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2002 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 246133 / % possible obs: 97 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 82.4 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. obs: 245475 / % possible obs: 96.7 % / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS Lowest resolution: 1.95 Å / % possible obs: 70.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HL5 Resolution: 1.9→27 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.366 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS SOME ATOMS THAT HAVE BEEN REFINED WITH AN OCCUPANCY OF 0.00
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.92 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→27 Å
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Refine LS restraints |
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