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Yorodumi- PDB-1jw8: 1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF P6 FORM OF MYOGLOBIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jw8 | ||||||
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Title | 1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF P6 FORM OF MYOGLOBIN | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / anisotropic refinement myoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Phillips Jr., G.N. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Authors: Kondrashov, D.A. / Zhang, W. / Aranda, R. / Stec, B. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jw8.cif.gz | 90.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jw8.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jw8_validation.pdf.gz | 800.9 KB | Display | wwPDB validaton report |
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Full document | 1jw8_full_validation.pdf.gz | 802.8 KB | Display | |
Data in XML | 1jw8_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | 1jw8_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/1jw8 ftp://data.pdbj.org/pub/pdb/validation_reports/jw/1jw8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17365.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB (Synthesized) / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-CMO / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9 Details: Ammonium sulfate, Tris, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction |
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Diffraction source |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.3→30 Å / Num. all: 49946 / Num. obs: 49946 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.051 / Net I/σ(I): 28 | |||||||||||||||||||||
Reflection shell | Resolution: 1.3→1.35 Å / Redundancy: 2 % / Rmerge(I) obs: 0.272 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→15 Å / Num. parameters: 14307 / Num. restraintsaints: 17825 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refine analyze | Num. disordered residues: 9 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→15 Å
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Refine LS restraints |
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