[English] 日本語
Yorodumi- PDB-1sxz: Reduced bovine superoxide dismutase at pH 5.0 complexed with azide -
+Open data
-Basic information
Entry | Database: PDB / ID: 1sxz | ||||||
---|---|---|---|---|---|---|---|
Title | Reduced bovine superoxide dismutase at pH 5.0 complexed with azide | ||||||
Components | PROTEIN (CU-ZN SUPEROXIDE DISMUTASE) | ||||||
Keywords | OXIDOREDUCTASE / SUPEROXIDE ACCEPTOR | ||||||
Function / homology | Function and homology information neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / : / locomotory behavior / regulation of mitochondrial membrane potential / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Ferraroni, M. / Rypniewski, W.R. / Bruni, B. / Orioli, P. / Wilson, K.S. / Mangani, S. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1998 Title: Crystallographic determination of reduced bovine superoxide dismutase at pH 5.0 and of anion binding to its active site Authors: Ferraroni, M. / Rypniewski, W.R. / Bruni, B. / Orioli, P. / Mangani, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sxz.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sxz.ent.gz | 55.9 KB | Display | PDB format |
PDBx/mmJSON format | 1sxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/1sxz ftp://data.pdbj.org/pub/pdb/validation_reports/sx/1sxz | HTTPS FTP |
---|
-Related structure data
Related structure data | 1sxcS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 15573.337 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ERYTHROCYTE / Cellular location: CYTOPLASM / Tissue: BLOOD / References: UniProt: P00442, superoxide dismutase |
---|
-Non-polymers , 5 types, 352 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 73 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Method: excess nitrogen atmosphere / pH: 5 Details: 20 % PEG6K, 20MM HEPES PH 5.0, SODIUM DITHIONITE (EXCESS), NITROGEN ATMOSPHERE, excess nitrogen atmosphere | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: free interface diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 213345 / % possible obs: 87.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.05→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 8.07 / % possible all: 85.5 |
Reflection | *PLUS Num. obs: 30955 / Num. measured all: 213345 |
Reflection shell | *PLUS % possible obs: 85.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SXC Resolution: 2.05→10 Å / σ(F): 0 Details: SIMILAR TO STRUCTURES 1SXA, 1SXB, 1SXC AND 1SXN, GLU 119 IN BOTH SUBUNITS APPEAR TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND THE ELECTRON DENSITY OCCURRING CLOSE ...Details: SIMILAR TO STRUCTURES 1SXA, 1SXB, 1SXC AND 1SXN, GLU 119 IN BOTH SUBUNITS APPEAR TO BE COVALENTLY MODIFIED. THE NATURE OF THE MODIFICATION IS UNKNOWN AND THE ELECTRON DENSITY OCCURRING CLOSE TO ITS SIDE CHAIN HAS BEEN TENTATIVELY MODELED AS CALCIUM IONS WITH 0.5 OCCUPANCY (IUM 154 A AND IUM 154 B). SEE PDB ENTRY 1SXC.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CCP4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.166 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |