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Yorodumi- PDB-5wjk: 2.0-Angstrom In situ Mylar structure of sperm whale myoglobin (SW... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wjk | ||||||||||||
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Title | 2.0-Angstrom In situ Mylar structure of sperm whale myoglobin (SWMb) at 293 K | ||||||||||||
Components | Myoglobin | ||||||||||||
Keywords | OXYGEN TRANSPORT / heme-bound / soluble protein | ||||||||||||
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 / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Physeter catodon (sperm whale) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Broecker, J. / Ou, W.-L. / Ernst, O.P. | ||||||||||||
Funding support | Germany, Canada, United States, 3items
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Citation | Journal: Nat Protoc / Year: 2018 Title: High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions. Authors: Broecker, J. / Morizumi, T. / Ou, W.L. / Klingel, V. / Kuo, A. / Kissick, D.J. / Ishchenko, A. / Lee, M.Y. / Xu, S. / Makarov, O. / Cherezov, V. / Ogata, C.M. / Ernst, O.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wjk.cif.gz | 51.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wjk.ent.gz | 34.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wjk ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wjk | HTTPS FTP |
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-Related structure data
Related structure data | 5vraC 5wktC 3e55S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17365.164 Da / Num. of mol.: 1 / Mutation: D122N 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 | ChemComp-CL / #4: Chemical | #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: 3.26 Å3/Da / Density % sol: 62.2 % / Description: red cubes and rods |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 9 Details: 10 mM Tris-HCl, 2.5 to 2.6 M (NH4)2SO4, 1 atm CO gas, seed solution in 10 mM Tris-HCl pH 9.0 and 3.2 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.84 Å / Num. obs: 14446 / % possible obs: 95 % / Redundancy: 1.8 % / Biso Wilson estimate: 26.9 Å2 / CC1/2: 0.89 / Net I/σ(I): 3.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Starting model: 3.0E+55 / Resolution: 2→45.835 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→45.835 Å
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Refine LS restraints |
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LS refinement shell |
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