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Yorodumi- PDB-1n9h: structure of microgravity-grown oxidized myoglobin mutant YQR (ISS6A) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n9h | ||||||
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Title | structure of microgravity-grown oxidized myoglobin mutant YQR (ISS6A) | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / globin fold / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Miele, A.E. / Sciara, G. / Federici, L. / Vallone, B. / Brunori, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Analysis of the effect of microgravity on protein crystal quality: the case of a myoglobin triple mutant. Authors: Miele, A.E. / Federici, L. / Sciara, G. / Draghi, F. / Brunori, M. / Vallone, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n9h.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n9h.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 1n9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n9h_validation.pdf.gz | 832.1 KB | Display | wwPDB validaton report |
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Full document | 1n9h_full_validation.pdf.gz | 832.2 KB | Display | |
Data in XML | 1n9h_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1n9h_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/1n9h ftp://data.pdbj.org/pub/pdb/validation_reports/n9/1n9h | HTTPS FTP |
-Related structure data
Related structure data | 1n9fC 1n9iC 1n9xC 1nazC 1f65S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the protein is a monomer |
-Components
#1: Protein | Mass: 17461.250 Da / Num. of mol.: 1 / Mutation: L29Y, H64Q, T67R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: myoglobin / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P02185 |
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#2: Chemical | ChemComp-OH / |
#3: Chemical | ChemComp-SO4 / |
#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: 3.07 Å3/Da / Density % sol: 59.91 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: ammonium sulfate, tris, EDTA, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.001 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.001 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→15 Å / Num. all: 34109 / Num. obs: 34109 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 12.29 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.5→1.52 Å / Redundancy: 2.21 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 10.2 / % possible all: 96.7 |
Reflection | *PLUS Num. obs: 31153 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1f65 Resolution: 1.8→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.32 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→15 Å
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Refine LS restraints |
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Refinement | *PLUS | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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