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Yorodumi- PDB-1ja8: Kinetic Analysis of Product Inhibition in Human Manganese Superox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ja8 | ||||||
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Title | Kinetic Analysis of Product Inhibition in Human Manganese Superoxide Dismutase | ||||||
Components | Manganese Superoxide DismutaseSuperoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / manganese / superoxide / disumtase / SOD / MnSOD / homo sapien / alpha-beta / two-domain / homotetramer / hydrogen bond network | ||||||
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 / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / superoxide metabolic process / negative regulation of fat cell differentiation / response to zinc ion / 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 / neuron development / response to hyperoxia / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / glutathione metabolic process / respiratory electron transport chain / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / removal of superoxide radicals / release of cytochrome c from mitochondria / post-embryonic development / liver development / response to activity / locomotory behavior / regulation of mitochondrial membrane potential / 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 / positive regulation of nitric oxide biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to oxidative stress / heart development / manganese ion binding / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Hearn, A.S. / Stroupe, M.E. / Cabelli, D.E. / Lepock, J.R. / Tainer, J.A. / Nick, H.S. / Silverman, D.S. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Kinetic analysis of product inhibition in human manganese superoxide dismutase. Authors: Hearn, A.S. / Stroupe, M.E. / Cabelli, D.E. / Lepock, J.R. / Tainer, J.A. / Nick, H.S. / Silverman, D.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ja8.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ja8.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ja8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/1ja8 ftp://data.pdbj.org/pub/pdb/validation_reports/ja/1ja8 | HTTPS FTP |
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-Related structure data
Related structure data | 1ap6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22117.980 Da / Num. of mol.: 2 / Mutation: W161A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHMNSDO4 / Production host: Escherichia coli (E. coli) / References: UniProt: P04179, superoxide dismutase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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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: 2.48 Å3/Da / Density % sol: 50.45 % | |||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 8 Details: ammonium sulfate, imidazole-malate, pH 8, VAPOR DIFFUSION, temperature 300K | |||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 8 / PH range high: 7.5 | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 132 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.773 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 9, 2000 |
Radiation | Monochromator: single crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.773 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 27115 / Num. obs: 26963 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AP6 Resolution: 2.12→17.82 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4108688.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.35 Å2 / ksol: 0.354 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.12→17.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.12→2.25 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % / Rfactor obs: 0.249 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.356 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.313 |