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Yorodumi- PDB-1ap5: TYR34->PHE MUTANT OF HUMAN MITOCHONDRIAL MANGANESE SUPEROXIDE DIS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ap5 | ||||||
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Title | TYR34->PHE MUTANT OF HUMAN MITOCHONDRIAL MANGANESE SUPEROXIDE DISMUTASE | ||||||
Components | MANGANESE SUPEROXIDE DISMUTASESuperoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / MANGANESE / TRANSIT PEPTIDE | ||||||
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 / regulation of mitochondrial membrane potential / liver development / locomotory behavior / response to activity / 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 / ISOMORPHOUS REFINEMENT / Resolution: 2.2 Å | ||||||
Authors | Guan, Y. / Borgstahl, G.E.O. / Tainer, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Crystal structure of Y34F mutant human mitochondrial manganese superoxide dismutase and the functional role of tyrosine 34. Authors: Guan, Y. / Hickey, M.J. / Borgstahl, G.E. / Hallewell, R.A. / Lepock, J.R. / O'Connor, D. / Hsieh, Y. / Nick, H.S. / Silverman, D.N. / Tainer, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ap5.cif.gz | 98.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ap5.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ap5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ap/1ap5 ftp://data.pdbj.org/pub/pdb/validation_reports/ap/1ap5 | HTTPS FTP |
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-Related structure data
Related structure data | 1ap6C 1abm S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8861, -0.4635, 0.0067), Vector: |
-Components
#1: Protein | Mass: 22217.111 Da / Num. of mol.: 2 / Mutation: Y34F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: KIDNEY / Organelle: MITOCHONDRIAMitochondrion / Production host: Escherichia coli (E. coli) / Strain (production host): SODASODB / References: UniProt: P04179, superoxide dismutase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % | ||||||||||||||||||||
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Crystal grow | pH: 7.8 / Details: 20% PEG 4000, pH 7.8 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Borgstahl, G.E.O., (1996) Biochemistry, 35, 4287. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: MONOCHROMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 20748 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.081 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.393 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REFINEMENT Starting model: PDB ENTRY 1ABM 1abm Resolution: 2.2→100 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 51.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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