+Open data
-Basic information
Entry | Database: PDB / ID: 1qnm | ||||||
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Title | HUMAN MANGANESE SUPEROXIDE DISMUTASE MUTANT Q143N | ||||||
Components | MANGANESE SUPEROXIDE DISMUTASESuperoxide dismutase | ||||||
Keywords | OXIDOREDUCTASE / MANGANESE SUPEROXIDE DISMUTASE / HMNSOD | ||||||
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 / superoxide anion generation / cellular response to ethanol / hydrogen peroxide biosynthetic process / response to manganese ion / negative regulation of fat cell differentiation / positive regulation of vascular associated smooth muscle cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / response to zinc ion / superoxide metabolic process / 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 / neuron development / response to axon injury / response to hyperoxia / removal of superoxide radicals / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to cadmium ion / glutathione metabolic process / response to electrical stimulus / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / respiratory electron transport chain / post-embryonic development / release of cytochrome c from mitochondria / locomotory behavior / regulation of mitochondrial membrane potential / liver development / response to activity / response to gamma radiation / response to hydrogen peroxide / Transcriptional activation of mitochondrial biogenesis / 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 / manganese ion binding / heart development / protein homotetramerization / negative regulation of neuron apoptotic process / response to lipopolysaccharide / response to hypoxia / mitochondrial matrix / positive regulation of cell migration / 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 / ISOMORPHOUS REFINEMENT / Resolution: 2.3 Å | ||||||
Authors | Guan, Y. / Tainer, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Probing the active site of human manganese superoxide dismutase: the role of glutamine 143. Authors: Hsieh, Y. / Guan, Y. / Tu, C. / Bratt, P.J. / Angerhofer, A. / Lepock, J.R. / Hickey, M.J. / 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 | 1qnm.cif.gz | 90.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qnm.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/1qnm ftp://data.pdbj.org/pub/pdb/validation_reports/qn/1qnm | HTTPS FTP |
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-Related structure data
Related structure data | 1abm 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.89, -0.4559, 0.0073), Vector: |
-Components
#1: Protein | Mass: 22219.084 Da / Num. of mol.: 2 / Mutation: Q143N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MUTATED RECOMBINANT HUMAN GENE / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PCMNSOD Gene (production host): MUTATED RECOMBINANT HUMAN GENE FOR MNSOD Production host: Escherichia coli (E. coli) / Strain (production host): SOD-- / 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: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: or sitting drop method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1997 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. obs: 18015 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rsym value: 0.092 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Rsym value: 0.335 / % possible all: 74.3 |
Reflection | *PLUS Lowest resolution: 99 Å / Num. measured all: 55987 / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Lowest resolution: 2.4 Å / % possible obs: 80 % |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS REFINEMENT Starting model: PDB ENTRY 1ABM 1abm Resolution: 2.3→100 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 38.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 10 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.4 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 obs: 0.198 / Rfactor Rfree: 0.294 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.334 |