+Open data
-Basic information
Entry | Database: PDB / ID: 2frf | ||||||
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Title | Horse Heart Myoglobin, Nitrite Adduct, Crystal Soak | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / Myoglobin / Nitrite / NO / NO2 / nitric oxide / heme / iron / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Copeland, D.M. / Soares, A.S. / West, A.H. / Richter-Addo, G.B. | ||||||
Citation | Journal: J.Inorg.Biochem. / Year: 2006 Title: Crystal structures of the nitrite and nitric oxide complexes of horse heart myoglobin. Authors: Copeland, D.M. / Soares, A.S. / 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 | 2frf.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2frf.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 2frf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/2frf ftp://data.pdbj.org/pub/pdb/validation_reports/fr/2frf | HTTPS FTP |
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-Related structure data
Related structure data | 2friC 2frjC 2frkC 1npfS S: Starting model for refinement 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 / Details: Heart Muscle / Source: (natural) Equus caballus (horse) / References: UniProt: P68082 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NO2 / | #4: Chemical | ChemComp-HEM / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Ammonium Sulfate/Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→10 Å / Num. all: 38095 / Num. obs: 37088 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.2→1.24 Å / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 4.34 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1NPF Resolution: 1.2→9.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.817 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.053 / ESU R Free: 0.053 / 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: 16.68 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→9.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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