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Yorodumi- PDB-2zkw: Crystal structure of human Cu-Zn superoxide dismutase mutant G85R... -
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-Basic information
Entry | Database: PDB / ID: 2zkw | |||||||||
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Title | Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group P21 | |||||||||
Components | Superoxide dismutase [Cu-Zn] | |||||||||
Keywords | OXIDOREDUCTASE / human Cu-Zn superoxide dismutase / ALS / FALS / metal-binding / disease mutation / E.C.1.15.1.1 / Amyotrophic lateral sclerosis / Antioxidant / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | |||||||||
Function / homology | Function and homology information action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus ...action potential initiation / neurofilament cytoskeleton organization / 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 / anterograde axonal transport / 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 / retrograde axonal transport / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / neuronal action potential / ectopic germ cell programmed cell death / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / : / positive regulation of superoxide anion generation / thymus development / regulation of mitochondrial membrane potential / locomotory behavior / positive regulation of cytokine production / determination of adult lifespan / placenta development / 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 / protein-folding chaperone binding / response to heat / 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: 1.9 Å | |||||||||
Authors | Yoshikawa, S. / Kukimoto-Niino, M. / Ito, K. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Shirouzu, M. / Urushitani, M. / Takahashi, R. ...Yoshikawa, S. / Kukimoto-Niino, M. / Ito, K. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Shirouzu, M. / Urushitani, M. / Takahashi, R. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | |||||||||
Citation | Journal: To be Published Title: Crystal structure of human Cu-Zn superoxide dismutase mutant G85R in space group P21 Authors: Yoshikawa, S. / Kukimoto-Niino, M. / Ito, K. / Chen, L. / Fu, Z.Q. / Chrzas, J. / Wang, B.C. / Shirouzu, M. / Urushitani, M. / Takahashi, R. / Yokoyama, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zkw.cif.gz | 68.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zkw.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 2zkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/2zkw ftp://data.pdbj.org/pub/pdb/validation_reports/zk/2zkw | HTTPS FTP |
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-Related structure data
Related structure data | 1hl5S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16470.348 Da / Num. of mol.: 2 / Mutation: G85R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOD1 / Plasmid: pGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00441, superoxide dismutase #2: Chemical | #3: Chemical | #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: 1.796609 Å3/Da / Density % sol: 31.537685 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 0.2M Ammonium iodide, 20%(w/v) PEG3350, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 31, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 17839 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.583 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.104 / Net I/σ(I): 10.367 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4.25 / Num. unique all: 1680 / Rsym value: 0.264 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HL5 Resolution: 1.9→33.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 185773.23 / Data cutoff low absF: 0 / 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: 54.2519 Å2 / ksol: 0.417534 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→33.46 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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