+Open data
-Basic information
Entry | Database: PDB / ID: 1f1g | ||||||
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Title | Crystal structure of yeast cuznsod exposed to nitric oxide | ||||||
Components | COPPER-ZINC SUPEROXIDE DISMUTASE | ||||||
Keywords | OXIDOREDUCTASE / Nitric Oxide / CuZnSOD | ||||||
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 / SYNCHROTRON / Resolution: 1.35 Å | ||||||
Authors | Hart, P.J. / Ogihara, N.L. / Liu, H. / Nersissian, A.M. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f1g.cif.gz | 381.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f1g.ent.gz | 318.5 KB | Display | PDB format |
PDBx/mmJSON format | 1f1g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f1g_validation.pdf.gz | 468.8 KB | Display | wwPDB validaton report |
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Full document | 1f1g_full_validation.pdf.gz | 477.8 KB | Display | |
Data in XML | 1f1g_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 1f1g_validation.cif.gz | 68.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/1f1g ftp://data.pdbj.org/pub/pdb/validation_reports/f1/1f1g | HTTPS FTP |
-Related structure data
Related structure data | 1b4lC 1b4tC 1f18C 1f1aC 1f1dC 1yazC 2jcwC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15874.587 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00445, superoxide dismutase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7 Details: ammonium sulfate, Tris-Hcl, NaCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.978 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→40 Å / Num. all: 1530112 / Num. obs: 233021 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.35→1.4 Å / Rmerge(I) obs: 0.223 / Num. unique all: 22837 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Resolution: 1.35→40 Å / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.35→40 Å
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Refine LS restraints |
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