+Open data
-Basic information
Entry | Database: PDB / ID: 2o58 | ||||||
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Title | Horse heart met manganese myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Horse heart / manganese myoglobin / oxidized form / manganese protoporphyrin IX / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / 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 | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 2o58.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o58.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 2o58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o58 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o58 | HTTPS FTP |
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-Related structure data
Related structure data | 2o5bC 2o5lC 2o5mC 2o5oC 2o5qC 2o5sC 2o5tC 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-MNR / | #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: 1.81 Å3/Da / Density % sol: 31.93 % |
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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: Dec 4, 2004 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→26.69 Å / Num. obs: 16239 / % possible obs: 99.3 % / Redundancy: 4.23 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.637 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.121 / 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: 17.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→19.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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