+Open data
-Basic information
Entry | Database: PDB / ID: 5z7f | |||||||||
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Title | Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative | |||||||||
Components | Myoglobin | |||||||||
Keywords | OXYGEN STORAGE / horse heart myoglobin mutant / V68A/I107Y / sulfide derivative | |||||||||
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 / Resolution: 1.9 Å | |||||||||
Authors | Yi, J. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Horse Heart Myoglobin Mutant -V68A/I107Y-Sulfide Derivative 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 | 5z7f.cif.gz | 47.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5z7f.ent.gz | 31.8 KB | Display | PDB format |
PDBx/mmJSON format | 5z7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/5z7f ftp://data.pdbj.org/pub/pdb/validation_reports/z7/5z7f | 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17005.479 Da / Num. of mol.: 1 / Mutation: V68A,I107Y 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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-Non-polymers , 6 types, 62 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-H2S / | ||||
#4: Chemical | ChemComp-NO2 / | ||||
#5: Chemical | #6: Chemical | ChemComp-GOL / | #7: 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: 1.77 Å3/Da / Density % sol: 30.59 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97845 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97845 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→60.38 Å / Num. obs: 8914 / % possible obs: 96.98 % / Redundancy: 3.2 % / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.9→1.949 Å |
-Processing
Software |
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Refinement | Resolution: 1.9→60.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.904 / SU B: 3.861 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.17 / 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: 16.078 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→60.38 Å
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Refine LS restraints |
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