+Open data
-Basic information
Entry | Database: PDB / ID: 5yce | |||||||||
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Title | Sperm whale myoglobin swMb | |||||||||
Components | Myoglobin | |||||||||
Keywords | OXYGEN STORAGE / Globin / Molecular Archaeology / Ancient protein / Protein evolution / Deep-sea adaptation | |||||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / 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: 0.77 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 | 5yce.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yce.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yce.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/5yce ftp://data.pdbj.org/pub/pdb/validation_reports/yc/5yce | HTTPS FTP |
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-Related structure data
Related structure data | 5ycgC 5ychC 5yciC 5ycjC 3rgkS S: Starting model for refinement 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: 17366.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | #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: 1.85 Å3/Da / Density % sol: 33.46 % |
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Crystal grow | Temperature: 291 K / Method: batch mode / Details: 76% saturated ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.8 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 0.77→10 Å / Num. obs: 148979 / % possible obs: 99.3 % / Redundancy: 4.5 % / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 0.77→0.81 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 5.6 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RGK Resolution: 0.77→9.949 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.16 / 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: 0.77→9.949 Å
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Refine LS restraints |
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