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Yorodumi- PDB-8vj8: X-ray Counterpart to Neutron Structure of Reduced Trp161Phe MnSOD -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vj8 | ||||||||||||
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Title | X-ray Counterpart to Neutron Structure of Reduced Trp161Phe MnSOD | ||||||||||||
Components | Superoxide dismutase [Mn], mitochondrial | ||||||||||||
Keywords | OXIDOREDUCTASE / MnSOD / SOD2 / PCET | ||||||||||||
Function / homology | Function and homology information acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress ...acetylcholine-mediated vasodilation involved in regulation of systemic arterial blood pressure / erythrophore differentiation / positive regulation of vascular associated smooth muscle cell differentiation involved in phenotypic switching / negative regulation of membrane hyperpolarization / detection of oxygen / positive regulation of hydrogen peroxide biosynthetic process / response to magnetism / response to silicon dioxide / response to L-ascorbic acid / response to isolation stress / intracellular oxygen homeostasis / response to selenium ion / response to superoxide / cellular response to ethanol / superoxide anion generation / hydrogen peroxide biosynthetic process / response to manganese ion / intrinsic apoptotic signaling pathway in response to oxidative stress / positive regulation of vascular associated smooth muscle cell apoptotic process / response to zinc ion / superoxide metabolic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / negative regulation of fat cell differentiation / superoxide dismutase / Detoxification of Reactive Oxygen Species / mitochondrial nucleoid / superoxide dismutase activity / negative regulation of vascular associated smooth muscle cell proliferation / hemopoiesis / response to immobilization stress / response to axon injury / response to hyperoxia / neuron development / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / response to electrical stimulus / negative regulation of fibroblast proliferation / glutathione metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / respiratory electron transport chain / post-embryonic development / release of cytochrome c from mitochondria / liver development / regulation of mitochondrial membrane potential / response to activity / locomotory behavior / response to gamma radiation / Transcriptional activation of mitochondrial biogenesis / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / multicellular organismal-level iron ion homeostasis / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of nitric oxide biosynthetic process / heart development / manganese ion binding / cellular response to oxidative stress / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / positive regulation of cell migration / mitochondrial matrix / response to xenobiotic stimulus / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / enzyme binding / mitochondrion / DNA binding / extracellular exosome / identical protein binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Biorxiv / Year: 2024 Title: Revealing the atomic and electronic mechanism of human manganese superoxide dismutase product inhibition. Authors: Azadmanesh, J. / Slobodnik, K. / Struble, L.R. / Lutz, W.E. / Coates, L. / Weiss, K.L. / Myles, D.A.A. / Kroll, T. / Borgstahl, G.E.O. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vj8.cif.gz | 128.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vj8.ent.gz | 80.6 KB | Display | PDB format |
PDBx/mmJSON format | 8vj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vj8_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 8vj8_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 8vj8_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 8vj8_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/8vj8 ftp://data.pdbj.org/pub/pdb/validation_reports/vj/8vj8 | HTTPS FTP |
-Related structure data
Related structure data | 8vhwC 8vhyC 8vj0C 8vj4C 8vj5C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1 / End auth comp-ID: LYS / End label comp-ID: LYS
NCS oper: (Code: givenMatrix: (-0.993160162059, 0.0138681574991, -0.115933458102), (0.00900368024674, -0.980868250921, -0.194464413395), (-0.116412311385, -0.194178136108, 0.974034406587)Vector: 71. ...NCS oper: (Code: given Matrix: (-0.993160162059, 0.0138681574991, -0.115933458102), Vector: |
-Components
#1: Protein | Mass: 22325.271 Da / Num. of mol.: 2 / Mutation: W161F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04179, superoxide dismutase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 46.68 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / Details: 1.8 M Potassium Phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 46105 / % possible obs: 97.6 % / Redundancy: 9.8 % / Biso Wilson estimate: 15.62 Å2 / CC1/2: 0.95 / Rpim(I) all: 0.036 / Net I/σ(I): 16.51 |
Reflection shell | Resolution: 1.7→1.74 Å / Num. unique obs: 4101 / CC1/2: 0.814 / Rpim(I) all: 0.036 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.95 Å / SU ML: 0.226 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1397 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.721612096049 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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