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Yorodumi- PDB-5m3s: Low-dose fixed target serial synchrotron crystallography structur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m3s | ||||||
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Title | Low-dose fixed target serial synchrotron crystallography structure of Metmyoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN BINDING / oxygen storage | ||||||
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: 1.8 Å | ||||||
Authors | Axford, D. / Owen, R.L. / Sherrell, D. / Muller-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 | 5m3s.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m3s.ent.gz | 36.7 KB | Display | PDB format |
PDBx/mmJSON format | 5m3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/5m3s ftp://data.pdbj.org/pub/pdb/validation_reports/m3/5m3s | HTTPS FTP |
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-Related structure data
Related structure data | 5o41C 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 on special symmetry positions |
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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 | ChemComp-SO4 / #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: 3.19 Å3/Da / Density % sol: 61.48 % |
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Crystal grow | Temperature: 294 K / Method: small tubes / Details: Tris, HCl, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2016 / Details: KB mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.76 Å / Num. obs: 24300 / % possible obs: 100 % / Redundancy: 75.2 % / CC1/2: 0.9779 / Rmerge(I) obs: 0.7614 / Net I/σ(I): 1.65 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 56.43 % / Rmerge(I) obs: 0.9583 / Mean I/σ(I) obs: 0.23 / CC1/2: 0.5887 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1a6m Resolution: 1.8→39.748 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.08 / 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: 1.8→39.748 Å
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Refine LS restraints |
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LS refinement shell |
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