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Yorodumi- PDB-4xcr: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xcr | ||||||
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Title | Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form, mutant I35A | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 / 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 / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / 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 / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / 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 / 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 / molecular replacement / Resolution: 3.602 Å | ||||||
Authors | Wang, H. / Logan, D.T. / Danielsson, J. / Mu, X. / Binolfi, A. / Theillet, F. / Bekei, B. / Lang, L. / Wennerstrom, H. / Selenko, P. / Oliveberg, M. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 Title: Thermodynamics of protein destabilization in live cells. Authors: Danielsson, J. / Mu, X. / Lang, L. / Wang, H. / Binolfi, A. / Theillet, F.X. / Bekei, B. / Logan, D.T. / Selenko, P. / Wennerstrom, H. / Oliveberg, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xcr.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xcr.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 4xcr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/4xcr ftp://data.pdbj.org/pub/pdb/validation_reports/xc/4xcr | HTTPS FTP |
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-Related structure data
Related structure data | 4bczS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 10948.210 Da / Num. of mol.: 2 / Mutation: I45A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00441, superoxide dismutase |
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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: 2.31 Å3/Da / Density % sol: 46.86 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.5 / Details: 0.1 M Bis Tris and 2.0 M ammonium sulfate / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 21, 2014 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 3.6→46.13 Å / Num. obs: 2203 / % possible obs: 92.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.326 / Net I/σ(I): 2.3 | |||||||||||||||
Reflection shell | Resolution: 3.6→3.94 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 2754 / Num. unique all: 533 / % possible all: 93.8 |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4BCZ Resolution: 3.602→46.133 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.62 Å2 / Biso mean: 58.2323 Å2 / Biso min: 42.38 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.602→46.133 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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