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Yorodumi- PDB-6n03: CO-bound Sperm Whale Myoglobin, room temperature structure, last ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6n03 | |||||||||
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Title | CO-bound Sperm Whale Myoglobin, room temperature structure, last 2 degrees of 5 degree total oscillation and 160 kGy dose | |||||||||
Components | Myoglobin, CO-bound | |||||||||
Keywords | OXYGEN TRANSPORT / oxygen transporter / myoglobin / TRANSPORT PROTEIN | |||||||||
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: 2.1 Å | |||||||||
Authors | Finke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: IUCrJ / Year: 2019 Title: Fixed-target serial oscillation crystallography at room temperature. Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6n03.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6n03.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 6n03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6n03_validation.pdf.gz | 820.7 KB | Display | wwPDB validaton report |
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Full document | 6n03_full_validation.pdf.gz | 823.9 KB | Display | |
Data in XML | 6n03_validation.xml.gz | 9 KB | Display | |
Data in CIF | 6n03_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/6n03 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/6n03 | HTTPS FTP |
-Related structure data
Related structure data | 6muhC 6muyC 6muzC 6mv0C 6mzzC 6n00C 6n02C 1vxaS 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: 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 | ChemComp-CMO / |
#4: Chemical | ChemComp-SO4 / |
#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: 2.03 Å3/Da / Density % sol: 39.37 % |
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Crystal grow | Temperature: 295 K / Method: batch mode Details: CO-SWMb crystals were homogenized in 10 mM Tris-HCl pH 9.0 and 3.2 M ammonium sulfate and washed two to three times with the same CO-saturated solution. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: G3 / Wavelength: 1.216 Å |
Detector | Type: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 4, 2018 |
Radiation | Monochromator: W/B4C multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.216 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40.16 Å / Num. obs: 8687 / % possible obs: 99.76 % / Redundancy: 17.1 % / Biso Wilson estimate: 48.59 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.0617 / Rrim(I) all: 0.2576 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 16.6 % / Mean I/σ(I) obs: 1.04 / Num. unique obs: 853 / CC1/2: 0.253 / Rpim(I) all: 1.234 / Rrim(I) all: 5.117 / % possible all: 99.65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VXA Resolution: 2.1→40.16 Å / SU ML: 0.3888 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 32.8356
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→40.16 Å
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Refine LS restraints |
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LS refinement shell |
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