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- PDB-2jcw: REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2jcw | |||||||||
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Title | REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE | |||||||||
![]() | CU/ZN SUPEROXIDE DISMUTASE | |||||||||
![]() | OXIDOREDUCTASE / SUPEROXIDE ACCEPTOR / COPPER / ZINC | |||||||||
Function / homology | ![]() superoxide dismutase complex / protein maturation by copper ion transfer / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / intracellular zinc ion homeostasis / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity ...superoxide dismutase complex / protein maturation by copper ion transfer / negative regulation of cellular respiration / fungal-type cell wall organization / Platelet degranulation / Detoxification of Reactive Oxygen Species / intracellular zinc ion homeostasis / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / intracellular copper ion homeostasis / removal of superoxide radicals / mitochondrial intermembrane space / peroxisome / protein stabilization / copper ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hart, P.J. / Balbirnie, M.M. / Ogihara, N.L. / Nersissian, A.M. / Weiss, M.S. / Valentine, J.S. / Eisenberg, D. | |||||||||
![]() | ![]() Title: A structure-based mechanism for copper-zinc superoxide dismutase. Authors: Hart, P.J. / Balbirnie, M.M. / Ogihara, N.L. / Nersissian, A.M. / Weiss, M.S. / Valentine, J.S. / Eisenberg, D. #1: ![]() Title: Unusual Trigonal-Planar Copper Configuration Revealed in the Atomic Structure of Yeast Copper-Zinc Superoxide Dismutase Authors: Ogihara, N.L. / Parge, H.E. / Hart, P.J. / Weiss, M.S. / Goto, J.J. / Crane, B.R. / Tsang, J. / Slater, K. / Roe, J.A. / Valentine, J.S. / Eisenberg, D. / Tainer, J.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 38.3 KB | Display | ![]() |
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PDB format | ![]() | 29.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 406.7 KB | Display | ![]() |
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Full document | ![]() | 407.9 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1b4lC ![]() 1b4tC ![]() 1f18C ![]() 1f1aC ![]() 1f1dC ![]() 1f1gC ![]() 1yazC ![]() 1sdyS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15743.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CARLBIOTECH, COPENHAGEN / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-CU1 / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.7 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1993 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→60 Å / Num. obs: 19256 / % possible obs: 82.3 % / Observed criterion σ(I): 0 / Redundancy: 4.53 % / Rsym value: 0.0988 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 40.8 |
Reflection | *PLUS Rmerge(I) obs: 0.0988 |
Reflection shell | *PLUS % possible obs: 40.8 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1SDY Resolution: 1.7→10 Å / σ(F): 0
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Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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