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Yorodumi- PDB-1yaz: AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yaz | ||||||
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Title | AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE | ||||||
Components | PROTEIN (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 / 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / OTHER / 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. / 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yaz.cif.gz | 45.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yaz.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yaz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yaz_validation.pdf.gz | 423.8 KB | Display | wwPDB validaton report |
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Full document | 1yaz_full_validation.pdf.gz | 427.5 KB | Display | |
Data in XML | 1yaz_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1yaz_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/1yaz ftp://data.pdbj.org/pub/pdb/validation_reports/ya/1yaz | HTTPS FTP |
-Related structure data
Related structure data | 1b4lC 1b4tC 1f18C 1f1aC 1f1dC 1f1gC 2jcwC 1jcw S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15743.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ROOM (298K) TEMPERATURE AZIDE-BOUND STRUCTURE WITH THE COPPER-IMIDAZOLATE BRIDGE INTACT Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Cellular location: CYTOPLASM / References: UniProt: P00445, superoxide dismutase |
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#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-AZI / |
#5: 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: 3.24 Å3/Da / Density % sol: 0.61 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Feb 15, 1996 |
Radiation | Monochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→90 Å / Num. obs: 22142 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.097 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.42 / % possible all: 89.7 |
Reflection | *PLUS Num. measured all: 133918 / Rmerge(I) obs: 0.097 |
Reflection shell | *PLUS % possible obs: 89.7 % / Rmerge(I) obs: 0.42 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: 1JCW 1jcw Resolution: 1.7→90 Å / Num. parameters: 5020 / Num. restraintsaints: 4358 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: SWAT | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→90 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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