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Yorodumi- PDB-3wfu: Crystal structure of horse heart myoglobin reconstituted with cob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wfu | ||||||
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Title | Crystal structure of horse heart myoglobin reconstituted with cobalt(I) tetradehydrocorrin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / globin fold / muscles | ||||||
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 / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Mizohata, E. / Morita, Y. / Oohora, K. / Hirata, K. / Ohbayashi, J. / Inoue, T. / Hisaeda, Y. / Hayashi, T. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2014 Title: Co(II)/Co(I) reduction-induced axial histidine-flipping in myoglobin reconstituted with a cobalt tetradehydrocorrin as a methionine synthase model. Authors: Hayashi, T. / Morita, Y. / Mizohata, E. / Oohora, K. / Ohbayashi, J. / Inoue, T. / Hisaeda, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wfu.cif.gz | 84 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wfu.ent.gz | 63.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/3wfu ftp://data.pdbj.org/pub/pdb/validation_reports/wf/3wfu | HTTPS FTP |
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-Related 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: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082 | ||||
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#2: Chemical | ChemComp-J1R / ( | ||||
#3: Chemical | ChemComp-J1S / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | THE COBALT COMPLEX J1R, J1S ARE CHARACTERIZED BY TETRA-COORDINATE CO IN 1+ OXIDATION STATE, AS ...THE COBALT COMPLEX J1R, J1S ARE CHARACTERI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M Tris-HCl, 3.4M ammonium sulfate, 10% treharose, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 22, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. obs: 25415 / % possible obs: 95.2 % / Redundancy: 2.7 % / Rsym value: 0.037 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 1.35→1.4 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.221 / % possible all: 92.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→15 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.426 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.34 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→15 Å
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