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Yorodumi- PDB-1ofj: RECOMBINANT SPERM WHALE MYOGLOBIN L29H/H64L/D122N MUTANT (WITH IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ofj | ||||||
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Title | RECOMBINANT SPERM WHALE MYOGLOBIN L29H/H64L/D122N MUTANT (WITH INITIATOR MET) | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT / HEME / MUSCLE PROTEIN / PEROXIDASE ACTIVITY | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / 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 | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Liong, E.C. / Phillips Jr., G.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Effects of the location of distal histidine in the reaction of myoglobin with hydrogen peroxide. Authors: Matsui, T. / Ozaki, S. / Liong, E. / Phillips Jr., G.N. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ofj.cif.gz | 47.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ofj.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1ofj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ofj_validation.pdf.gz | 805.8 KB | Display | wwPDB validaton report |
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Full document | 1ofj_full_validation.pdf.gz | 807.1 KB | Display | |
Data in XML | 1ofj_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1ofj_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/1ofj ftp://data.pdbj.org/pub/pdb/validation_reports/of/1ofj | HTTPS FTP |
-Related 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: 17365.164 Da / Num. of mol.: 1 / Mutation: INITIATOR MET, L29H, H64L, D122N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
Sequence details | THIS STRUCTURE HAS FOUR DIFFERENCES RELATIVE TO THE NATIVE SPERM WHALE PROTEIN: AN INITIATOR ...THIS STRUCTURE HAS FOUR DIFFERENCE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.32 % | |||||||||||||||||||||||||
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Crystal grow | pH: 9 / Details: pH 9.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. obs: 20475 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.048 |
-Processing
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Refinement | Resolution: 1.8→5 Å / Isotropic thermal model: RESTRAINED / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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