+Open data
-Basic information
Entry | Database: PDB / ID: 1mfm | ||||||
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Title | MONOMERIC HUMAN SOD MUTANT F50E/G51E/E133Q AT ATOMIC RESOLUTION | ||||||
Components | PROTEIN (COPPER,ZINC SUPEROXIDE DISMUTASE) | ||||||
Keywords | OXIDOREDUCTASE / SUPEROXIDE ACCEPTOR / MONOMERIC MUTANT | ||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | ||||||
Authors | Ferraroni, M. / Rypniewski, W. / Wilson, K.S. / Orioli, P.L. / Viezzoli, M.S. / Banci, L. / Bertini, I. / Mangani, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: The crystal structure of the monomeric human SOD mutant F50E/G51E/E133Q at atomic resolution. The enzyme mechanism revisited. Authors: Ferraroni, M. / Rypniewski, W. / Wilson, K.S. / Viezzoli, M.S. / Banci, L. / Bertini, I. / Mangani, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mfm.cif.gz | 52.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mfm.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mf/1mfm ftp://data.pdbj.org/pub/pdb/validation_reports/mf/1mfm | HTTPS FTP |
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-Related structure data
Related structure data | 1sosS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15832.447 Da / Num. of mol.: 1 / Mutation: C6A,F50E,G51E,C111S,E133Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: SOD1 / Cellular location (production host): PERIPLASM / Gene (production host): HSOD / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP 1 (STRATAGENE) / References: UniProt: P00441, superoxide dismutase |
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-Non-polymers , 5 types, 296 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-CU / | ||||
#4: Chemical | ChemComp-CD / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: PEG 6000 15%, CDCL2 200-400 MM, TRIS 100MM, PH=8, pH 8.0 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.89 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: SEGMENTED MIRROR |
Radiation | Monochromator: TRIANGULAR GE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 |
Reflection | Resolution: 1→20 Å / Num. obs: 681833 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rsym value: 0.061 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.02→1.04 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.513 / % possible all: 98 |
Reflection | *PLUS Num. obs: 69841 / Num. measured all: 681833 / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 98 % / Rmerge(I) obs: 0.247 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SOS Resolution: 1.02→20 Å / Num. parameters: 12921 / Num. restraintsaints: 15655 / σ(F): 0
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Refine analyze | Num. disordered residues: 19 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-96 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / Rfactor Rwork: 0.118 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |