+Open data
-Basic information
Entry | Database: PDB / ID: 5ycg | |||||||||
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Title | Ancestral myoglobin aMbWp of Pakicetus relative | |||||||||
Components | Ancestral myoglobin aMbWp of Pakicetus relative | |||||||||
Keywords | OXYGEN STORAGE / Globin / Molecular Archaeology / Ancient protein / Protein evolution / Deep-sea adaptation | |||||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | |||||||||
Biological species | Physeter catodon (sperm whale) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K. / Nakagawa, T. / Tsuneshige, A. / Shirai, T. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Sci Rep / Year: 2018 Title: Tracing whale myoglobin evolution by resurrecting ancient proteins. Authors: Isogai, Y. / Imamura, H. / Nakae, S. / Sumi, T. / Takahashi, K.I. / Nakagawa, T. / Tsuneshige, A. / Shirai, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ycg.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ycg.ent.gz | 32 KB | Display | PDB format |
PDBx/mmJSON format | 5ycg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5ycg ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5ycg | HTTPS FTP |
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-Related structure data
Related structure data | 5yceC 5ychC 5yciC 5ycjSC C: citing same article (ref.) S: Starting model for refinement |
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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: 17429.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Physeter catodon (sperm whale) / References: UniProt: P68082*PLUS |
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#2: Chemical | ChemComp-HEM / |
#3: 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: 2.59 Å3/Da / Density % sol: 52.45 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3.5 M ammonium sulfate solution for a 0.5 mL reservoir, and a mixture of 2 uL of the reservoir solution and 2 uL of protein solution in a 50 mM Tris-HCl (pH 8.0) buffer containing 2% (w/v) aMbWp |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→23.631 Å / Num. obs: 7124 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 21.3 / Num. unique obs: 1034 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5YCJ Resolution: 2.4→23.631 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→23.631 Å
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Refine LS restraints |
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LS refinement shell |
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