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Open data
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Basic information
Entry | Database: PDB / ID: 4nip | ||||||
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Title | GVIGIAQ segment 147-153 from Human Superoxide Dismutase | ||||||
![]() | GVTGIAQ segment from Superoxide dismutase [Cu-Zn] | ||||||
![]() | PROTEIN FIBRIL / steric zipper / cross-beta spine / amyloid fiber | ||||||
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 / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...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 / peripheral nervous system myelin maintenance / 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 / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / heart contraction / superoxide metabolic process / positive regulation of catalytic activity / superoxide dismutase / negative regulation of reproductive process / negative regulation of developmental process / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / neuronal action potential / ovarian follicle development / positive regulation of phagocytosis / axon cytoplasm / embryo implantation / dendrite cytoplasm / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / reactive oxygen species metabolic process / removal of superoxide radicals / glutathione 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 / placenta development / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / Platelet degranulation / peroxisome / gene expression / protein-folding chaperone binding / 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 / zinc ion binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sievers, S.A. / Sawaya, M.R. / Eisenberg, D. / Ivanova, M.I. | ||||||
![]() | ![]() Title: Aggregation-triggering segments of SOD1 fibril formation support a common pathway for familial and sporadic ALS. Authors: Ivanova, M.I. / Sievers, S.A. / Guenther, E.L. / Johnson, L.M. / Winkler, D.D. / Galaleldeen, A. / Sawaya, M.R. / Hart, P.J. / Eisenberg, D.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 | ![]() | 8.9 KB | Display | ![]() |
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PDB format | ![]() | 5.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.8 KB | Display | ![]() |
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Full document | ![]() | 405.8 KB | Display | |
Data in XML | ![]() | 2.3 KB | Display | |
Data in CIF | ![]() | 2.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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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Details | biological unit is a pair of beta-sheets. One sheet is composed of symmetry operators X,Y,Z; X,Y-1,Z; X,Y+1,Z; X,Y-2,Z; X,Y+2,Z, etc.: the opposing sheet is composed of symmetry operators 1/2-x,1/2+y,-z; 1/2-x,-1/2+y,-z; 1/2-x, 3/2+y,-z; 1/2-x,-3/2+y,-z; 1/2-x, 5/2+y,-z, etc. |
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Components
#1: Protein/peptide | Mass: 656.772 Da / Num. of mol.: 1 / Fragment: UNP Residues 148-154 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 25.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1 M sodium acetate pH 4.5, 1.75 M ammonium sulfate, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2007 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: cryogenically-cooled single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.895432 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→90 Å / Num. all: 415 / Num. obs: 415 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.144 / Χ2: 1.515 / Net I/σ(I): 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]()
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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 max: 40.82 Å2 / Biso mean: 17.1302 Å2 / Biso min: 2.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→24.85 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.951 Å / Total num. of bins used: 20
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