+Open data
-Basic information
Entry | Database: PDB / ID: 2o5t | ||||||
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Title | Cobalt horse heart myoglobin, oxidized | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Cobalt protoporphyrin IX / cobalt myoglobin / oxidized form / horse heart / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Richter-Addo, G.B. / Zahran, Z.N. / Chooback, L. / Copeland, D.M. / West, A.H. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2008 Title: Crystal structures of manganese- and cobalt-substituted myoglobin in complex with NO and nitrite reveal unusual ligand conformations. Authors: Zahran, Z.N. / Chooback, L. / Copeland, D.M. / West, A.H. / Richter-Addo, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o5t.cif.gz | 47.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o5t.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 2o5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2o5t_validation.pdf.gz | 809.4 KB | Display | wwPDB validaton report |
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Full document | 2o5t_full_validation.pdf.gz | 813.9 KB | Display | |
Data in XML | 2o5t_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 2o5t_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o5t ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o5t | HTTPS FTP |
-Related structure data
Related structure data | 2o58C 2o5bC 2o5lC 2o5mC 2o5oC 2o5qC 2o5sC 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
#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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#2: Chemical | #3: Chemical | ChemComp-COH / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 31.89 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 296K Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 1, 2006 |
Radiation | Monochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.93 Å / Num. obs: 14921 / Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→26.51 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.165 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.125 / 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: 21.588 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→26.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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