+Open data
-Basic information
Entry | Database: PDB / ID: 8vhy | ||||||||||||
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Title | Neutron Structure of Reduced Trp161Phe MnSOD | ||||||||||||
Components | Superoxide dismutase [Mn], mitochondrial | ||||||||||||
Keywords | OXIDOREDUCTASE / MnSOD / SOD2 / Product-Inhibition / 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 | NEUTRON DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
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. | ||||||||||||
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 | 8vhy.cif.gz | 229.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vhy.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 8vhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vhy_validation.pdf.gz | 339.3 KB | Display | wwPDB validaton report |
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Full document | 8vhy_full_validation.pdf.gz | 339.7 KB | Display | |
Data in XML | 8vhy_validation.xml.gz | 10 KB | Display | |
Data in CIF | 8vhy_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/8vhy ftp://data.pdbj.org/pub/pdb/validation_reports/vh/8vhy | HTTPS FTP |
-Related structure data
Related structure data | 8vhwC 8vj0C 8vj4C 8vj5C 8vj8C 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
#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: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 1.93 M Potassium Phosphate |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SPALLATION SOURCE / Site: ORNL Spallation Neutron Source / Beamline: MANDI / Wavelength: 2-4 | |||||||||
Detector | Type: ORNL ANGER CAMERA / Detector: DIFFRACTOMETER / Date: Jan 22, 2022 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→14.74 Å / Num. obs: 18253 / % possible obs: 92.6 % / Redundancy: 4.2 % / Biso Wilson estimate: -1.09 Å2 / CC1/2: 0.84 / Rpim(I) all: 0.122 / Net I/σ(I): 4.8 | |||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1632 / CC1/2: 0.407 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→14.74 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.67 / Phase error: 24.0492 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 11.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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