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Yorodumi- PDB-1b4l: 15 ATMOSPHERE OXYGEN YEAST CU/ZN SUPEROXIDE DISMUTASE ROOM TEMPER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b4l | ||||||
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Title | 15 ATMOSPHERE OXYGEN YEAST CU/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 oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / 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 / cellular detoxification / superoxide metabolic process ...oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor / 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 / cellular detoxification / superoxide metabolic process / superoxide dismutase / superoxide dismutase activity / intracellular copper ion homeostasis / removal of superoxide radicals / mitochondrial intermembrane space / cellular response to oxidative stress / 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 / SYNCHROTRON / OTHER / Resolution: 1.8 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 | 1b4l.cif.gz | 41.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b4l.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 1b4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b4l_validation.pdf.gz | 413.4 KB | Display | wwPDB validaton report |
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Full document | 1b4l_full_validation.pdf.gz | 413.8 KB | Display | |
Data in XML | 1b4l_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1b4l_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b4l ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b4l | HTTPS FTP |
-Related structure data
Related structure data | 1b4tC 1f18C 1f1aC 1f1dC 1f1gC 1yazC 2jcwC 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
#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 |
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#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-ZN / |
#4: 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: 3.25 Å3/Da / Density % sol: 61.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
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: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 16745 / % possible obs: 87.7 % / Observed criterion σ(I): 0 / Redundancy: 3.88 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.048 / Net I/σ(I): 22 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 7.4 / Rsym value: 0.148 / % possible all: 90.5 |
Reflection | *PLUS Num. measured all: 64930 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / % possible obs: 90.5 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.8→10 Å / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.279 / Rfactor Rwork: 0.264 |