[English] 日本語
Yorodumi- PDB-2jcw: REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jcw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | REDUCED BRIDGE-BROKEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE | |||||||||
Components | CU/ZN SUPEROXIDE DISMUTASE | |||||||||
Keywords | OXIDOREDUCTASE / SUPEROXIDE ACCEPTOR / COPPER / ZINC | |||||||||
Function / homology | Function and homology information superoxide dismutase complex / protein maturation by copper ion transfer / negative regulation of cellular respiration / fungal-type cell wall organization / Detoxification of Reactive Oxygen Species / Platelet degranulation / 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 / Detoxification of Reactive Oxygen Species / Platelet degranulation / 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 | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Hart, P.J. / Balbirnie, M.M. / Ogihara, N.L. / Nersissian, A.M. / Weiss, M.S. / Valentine, J.S. / Eisenberg, D. | |||||||||
Citation | Journal: Biochemistry / Year: 1999 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: Journal: Biochemistry / Year: 1996 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jcw.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jcw.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jcw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jcw ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jcw | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15743.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: CARLBIOTECH, COPENHAGEN / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / References: UniProt: P00445, superoxide dismutase |
---|---|
#2: Chemical | ChemComp-CU1 / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.26 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.7 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SDY Resolution: 1.7→10 Å / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|