+Open data
-Basic information
Entry | Database: PDB / ID: 5z7e | |||||||||
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Title | Horse Heart Myoglobin Mutant - H93M | |||||||||
Components | Myoglobin | |||||||||
Keywords | OXYGEN STORAGE / horse heart myoglobin mutant / H93M | |||||||||
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 / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding ...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 / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Yi, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Horse Heart Myoglobin Mutant - H93M Authors: Yi, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5z7e.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z7e.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 5z7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/5z7e ftp://data.pdbj.org/pub/pdb/validation_reports/z7/5z7e | 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: 16976.562 Da / Num. of mol.: 1 / Mutation: H93M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P68082 | ||||
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#2: Chemical | ChemComp-NO2 / | ||||
#3: Chemical | #4: Chemical | ChemComp-HEM / | #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: 1.81 Å3/Da / Density % sol: 31.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.5-3.0M ammonium sulfate, 0.1M Tris / PH range: 7.0-9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 24, 2016 |
Radiation | 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→60.89 Å / Num. obs: 10965 / % possible obs: 99.5 % / Redundancy: 3.2 % / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.8→1.847 Å |
-Processing
Software |
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Refinement | Resolution: 1.8→60.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.89 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.126 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.982 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→60.89 Å
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Refine LS restraints |
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