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Yorodumi- PDB-5xl0: met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xl0 | ||||||
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Title | met-aquo form of sperm whale myoglobin reconstituted with 7-PF, a heme possesseing CF3 group as side chain | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / sperm whale / myoglobin / Trifluoromethyl Group / fluorinated heme / heme orientational disorder | ||||||
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: 1.25 Å | ||||||
Authors | Kanai, Y. / Harada, A. / Shibata, T. / Nishimura, R. / Namiki, K. / Watanabe, M. / Nakamura, S. / Yumoto, F. / Senda, T. / Suzuki, A. ...Kanai, Y. / Harada, A. / Shibata, T. / Nishimura, R. / Namiki, K. / Watanabe, M. / Nakamura, S. / Yumoto, F. / Senda, T. / Suzuki, A. / Neya, S. / Yamamoto, Y. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Characterization of Heme Orientational Disorder in a Myoglobin Reconstituted with a Trifluoromethyl-Group-Substituted Heme Cofactor Authors: Kanai, Y. / Harada, A. / Shibata, T. / Nishimura, R. / Namiki, K. / Watanabe, M. / Nakamura, S. / Yumoto, F. / Senda, T. / Suzuki, A. / Neya, S. / Yamamoto, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xl0.cif.gz | 50.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xl0.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xl/5xl0 ftp://data.pdbj.org/pub/pdb/validation_reports/xl/5xl0 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17049.771 Da / Num. of mol.: 1 / Fragment: UNP residues 2-152 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-89R / | ||
#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: 1.92 Å3/Da / Density % sol: 35.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: 2.9 M ammonium sulfate, 0.1 M Bis-Tris-propane HCl buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 28, 2014 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→33.04 Å / Num. obs: 72066 / % possible obs: 99.8 % / Redundancy: 6.3 % / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.25→1.27 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→30.92 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→30.92 Å
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Refine LS restraints |
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LS refinement shell |
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