[English] 日本語
Yorodumi- PDB-4bcz: Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII dele... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bcz | ||||||
---|---|---|---|---|---|---|---|
Title | Monomeric Human Cu,Zn Superoxide dismutase, loops IV and VII deleted, apo form. | ||||||
Components | SUPEROXIDE DISMUTASE [CU-ZN] | ||||||
Keywords | OXIDOREDUCTASE / CU/ZN SOD1 / MONOMERIC MUTANT / DISEASE MUTATION / METAL BINDING / NEURODEGENERATION / ALS | ||||||
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 / glutathione metabolic process / axon cytoplasm / 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 / locomotory behavior / regulation of mitochondrial membrane potential / 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: 1.93 Å | ||||||
Authors | Saraboji, K. / Awad, W. / Danielsson, J. / Lang, L. / Kurnik, M. / Marklund, S.L. / Oliveberg, M. / Logan, D.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Global Structural Motions from the Strain of a Single Hydrogen Bond. Authors: Danielsson, J. / Awad, W. / Saraboji, K. / Kurnik, M. / Lang, L. / Leinartaite, L. / Marklund, S.L. / Logan, D.T. / Oliveberg, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bcz.cif.gz | 94 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bcz.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 4bcz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/4bcz ftp://data.pdbj.org/pub/pdb/validation_reports/bc/4bcz | HTTPS FTP |
---|
-Related structure data
Related structure data | 4bcyC 4bd4C 2xjkS 4a7r S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.338, -0.9408, -0.02539), Vector: |
-Components
#1: Protein | Mass: 10990.290 Da / Num. of mol.: 2 / Fragment: RESIDUES 2049,83-124,141-154 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00441, superoxide dismutase #2: Water | ChemComp-HOH / | Sequence details | MUTATIONS C6A, C111A, C146S DELETION OF RESIDUES 49-81 AND 124-139) AND REPLACEMEN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % / Description: NONE |
---|---|
Crystal grow | Temperature: 293 K / Details: 30% PEG 1500, 0.1M MIB BUFFER, PH 4.0, 20 C |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 |
Detector | Type: MARRESEARCH 165MM / Detector: CCD / Date: Mar 15, 2011 / Details: HORIZONTALLY FOCUSING MIRROR |
Radiation | Monochromator: BENT SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0379 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→30 Å / Num. obs: 14115 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 28.83 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.93→1.98 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XJK Resolution: 1.93→30 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 23.59 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.6 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|