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Yorodumi- PDB-5o41: Low-dose fixed target serial synchrotron crystallography structur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o41 | |||||||||
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Title | Low-dose fixed target serial synchrotron crystallography structure of sperm whale myoglobin | |||||||||
Components | Myoglobin | |||||||||
Keywords | OXYGEN BINDING / oxygen storage | |||||||||
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: 1.8 Å | |||||||||
Authors | Owen, R.L. / Axford, D. / Sherrell, D. / Mueller-Werkmeister, H. | |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Low-dose fixed-target serial synchrotron crystallography. Authors: Owen, R.L. / Axford, D. / Sherrell, D.A. / Kuo, A. / Ernst, O.P. / Schulz, E.C. / Miller, R.J. / Mueller-Werkmeister, H.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o41.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o41.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 5o41.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/5o41 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o41 | HTTPS FTP |
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-Related structure data
Related structure data | 5m3sC 1a6mS 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: 17365.164 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: Chemical | ChemComp-CMO / | #5: 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: 2.16 Å3/Da / Density % sol: 43.16 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / Details: Tris, HCl, ammonium sulfate, CO |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.35 Å / Num. obs: 14552 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 0.936 / Rmerge(I) obs: 0.7947 / Net I/σ(I): 4.27 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 18.3 % / Rmerge(I) obs: 0.9256 / Mean I/σ(I) obs: 0.36 / CC1/2: 0.475 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a6m Resolution: 1.8→42.333 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.47
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.333 Å
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Refine LS restraints |
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LS refinement shell |
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