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- PDB-1yaz: AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yaz | ||||||
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Title | AZIDE-BOUND YEAST CU(II)/ZN SUPEROXIDE DISMUTASE ROOM TEMPERATURE (298K) STRUCTURE | ||||||
![]() | PROTEIN (CU/ZN SUPEROXIDE DISMUTASE) | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() 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. / 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 | ![]() | 45.1 KB | Display | ![]() |
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PDB format | ![]() | 30.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1b4lC ![]() 1b4tC ![]() 1f18C ![]() 1f1aC ![]() 1f1dC ![]() 1f1gC ![]() 2jcwC ![]() 1jcw 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 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) ![]() ![]() ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() 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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