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Yorodumi- PDB-5azq: Crystal structure of cyano-cobalt(III) tetradehydrocorrin in the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5azq | ||||||
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Title | Crystal structure of cyano-cobalt(III) tetradehydrocorrin in the heme pocket of horse heart myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / globin fold / muscles / redox enzyme | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å | ||||||
Authors | Mizohata, E. / Morita, Y. / Oohora, K. / Inoue, T. / Hayashi, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Inorg.Chem. / Year: 2016 Title: Crystal Structures and Coordination Behavior of Aqua- and Cyano-Co(III) Tetradehydrocorrins in the Heme Pocket of Myoglobin Authors: Morita, Y. / Oohora, K. / Mizohata, E. / Sawada, A. / Kamachi, T. / Yoshizawa, K. / Inoue, T. / Hayashi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5azq.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5azq.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 5azq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5azq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5azq_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5azq_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 5azq_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/5azq ftp://data.pdbj.org/pub/pdb/validation_reports/az/5azq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: heart / References: UniProt: P68082 |
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-Non-polymers , 5 types, 146 molecules
#2: Chemical | ChemComp-J1R / ( | ||
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#3: Chemical | ChemComp-J1S / ( | ||
#4: Chemical | ChemComp-CYN / | ||
#5: Chemical | #6: 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: 1.8 Å3/Da / Density % sol: 31.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: ammonium sulfate, Tris-HCl, trehalose |
-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: Nov 5, 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: 1.4→50 Å / Num. obs: 23585 / % possible obs: 97.8 % / Redundancy: 3.61 % / Rsym value: 0.056 / Net I/σ(I): 22.6 |
Reflection shell | Resolution: 1.4→1.45 Å / Mean I/σ(I) obs: 2.4 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.968 / SU B: 3.658 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.07 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.802 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→50 Å
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