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Yorodumi- PDB-1luv: CATALYTIC AND STRUCTURAL EFFECTS OF AMINO-ACID SUBSTITUTION AT HI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1luv | ||||||
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Title | CATALYTIC AND STRUCTURAL EFFECTS OF AMINO-ACID SUBSTITUTION AT HIS 30 IN HUMAN MANGANESE SUPEROXIDE DISMUTASE: INSERTION OF VAL CGAMMA INTO THE SUBSTRATE ACCESS CHANNEL | ||||||
Components | Superoxide dismutase [Mn] | ||||||
Keywords | OXIDOREDUCTASE / human manganese superoxide dismutase / wild type / high resolution / MnSOD / Mn | ||||||
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: 1.85 Å | ||||||
Authors | Hearn, A.S. / Stroupe, M.E. / Ramilo, C.A. / Luba, J.P. / Cabelli, D.E. / Tainer, J.A. / Silverman, D.N. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Catalytic and structural effects of amino acid substitution at histidine 30 in human manganese superoxide dismutase: insertion of valine C gamma into the substrate access channel Authors: Hearn, A.S. / Stroupe, M.E. / Cabelli, D.E. / Ramilo, C.A. / Luba, J.P. / 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 | 1luv.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1luv.ent.gz | 74.2 KB | Display | PDB format |
PDBx/mmJSON format | 1luv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/1luv ftp://data.pdbj.org/pub/pdb/validation_reports/lu/1luv | HTTPS FTP |
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-Related structure data
-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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Details | The asymmetric unit contains a dimer; to generate the active tetramer apply the following rotation and translation to chains A and B 0.500000 -0.866025 0.000000 -0.866025 -0.500000 0.000000 0.000000 0.000000 -1.00000 translation: 39.82150 68.97286 201.36833 |
-Components
#1: Protein | Mass: 22233.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): QC774 (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: 2.5 Å3/Da / Density % sol: 50.77 % | ||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM imidazole/malate, 2.5M ammonium sulfate, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 8 / PH range high: 7 | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 272 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 20, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. all: 39262 / Num. obs: 39262 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.46 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.078 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.29 / Num. unique all: 1932 / Rsym value: 0.465 / % possible all: 99 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % possible obs: 98 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.078 |
Reflection shell | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: hMnSOD Y34F Resolution: 1.85→19.91 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.1922 Å2 / ksol: 0.37124 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze | Luzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.26 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.311 |