+Open data
-Basic information
Entry | Database: PDB / ID: 3ba2 | ||||||
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Title | Cyanide bound Chlorin substituted Myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | TRANSPORT PROTEIN / Myoglobin / Heme / Chlorin / Cyanide / CN / reconstituted / Iron / Metal-binding / Muscle protein / Oxygen transport / Transport | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Yi, J. / Copeland, D.M. / Richter-Addo, G.B. | ||||||
Citation | Journal: To be Published Title: Cyanide bound Chlorin substituted Myoglobin Authors: Yi, J. / 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 | 3ba2.cif.gz | 47 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ba2.ent.gz | 32.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ba2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/3ba2 ftp://data.pdbj.org/pub/pdb/validation_reports/ba/3ba2 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: Horse Heart / Source: (natural) Equus caballus (horse) / References: UniProt: P68082 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CYN / | #4: Chemical | ChemComp-HKL / | #5: 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: 1.89 Å3/Da / Density % sol: 35.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 3.1M ammonium sulfate, 100mM 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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 12, 2007 / Details: Osmic blue | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→22.35 Å / Num. all: 12043 / Num. obs: 11926 / % possible obs: 99 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.034 / Χ2: 0.98 / Net I/σ(I): 21.9 / Scaling rejects: 310 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.343 / Cor.coef. Fo:Fc: 0.703
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.8 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.147 / 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: 14.551 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→22.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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