+Open data
-Basic information
Entry | Database: PDB / ID: 1yog | ||||||
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Title | COBALT MYOGLOBIN (DEOXY) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / MUSCLE | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.65 Å | ||||||
Authors | Brucker, E.A. / Phillips Jr., G.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1996 Title: High resolution crystal structures of the deoxy, oxy, and aquomet forms of cobalt myoglobin. Authors: Brucker, E.A. / Olson, J.S. / Phillips Jr., G.N. / Dou, Y. / Ikeda-Saito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yog.cif.gz | 45.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yog.ent.gz | 31.4 KB | Display | PDB format |
PDBx/mmJSON format | 1yog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yog_validation.pdf.gz | 479.4 KB | Display | wwPDB validaton report |
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Full document | 1yog_full_validation.pdf.gz | 484.1 KB | Display | |
Data in XML | 1yog_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | 1yog_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yog ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yog | HTTPS FTP |
-Related 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: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: RECONSTITUTED WITH COBALT PROTOPORPHYRIN IX (DEOXY) Source: (natural) Physeter catodon (sperm whale) / Tissue: MUSCLE / References: UniProt: P02185 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-COH / |
#4: Water | ChemComp-HOH / |
Nonpolymer details | THIS STRUCTURE HAS ONE DIFFERENCE RELATIVE TO THE NATIVE SPERM WHALE PROTEIN: THE HEME UNIT (IRON ...THIS STRUCTURE HAS ONE DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.45 % | |||||||||||||||
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Crystal grow | *PLUS Temperature: 17 ℃ / Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 62314 / % possible obs: 81.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.101 |
Reflection | *PLUS Num. obs: 12618 / Num. measured all: 62314 |
-Processing
Software |
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Refinement | Resolution: 1.65→5 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.65→5 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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