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Yorodumi- PDB-1ufp: Crystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ufp | ||||||
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Title | Crystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me2-salophen)/apo-wild type Myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / myoglobin / Schiff base / iron / salophen / metalloprotein / 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 / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Ueno, T. / Ohashi, M. / Kono, M. / Kondo, K. / Suzuki, A. / Yamane, T. / Watanabe, Y. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2004 Title: Crystal Structures of Artificial Metalloproteins: Tight Binding of Fe(III)(Schiff-Base) by Mutation of Ala71 to Gly in Apo-Myoglobin Authors: Ueno, T. / Ohashi, M. / Kono, M. / Kondo, K. / Suzuki, A. / Yamane, T. / Watanabe, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ufp.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ufp.ent.gz | 33.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ufp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ufp_validation.pdf.gz | 374.7 KB | Display | wwPDB validaton report |
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Full document | 1ufp_full_validation.pdf.gz | 377.2 KB | Display | |
Data in XML | 1ufp_validation.xml.gz | 5 KB | Display | |
Data in CIF | 1ufp_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/1ufp ftp://data.pdbj.org/pub/pdb/validation_reports/uf/1ufp | HTTPS FTP |
-Related structure data
Related structure data | 1ufjSC S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 17366.148 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: puc19 / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-PO4 / #3: 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: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: sodium, potassium phosphate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 3, 2002 |
Radiation | Monochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. all: 8790 / Num. obs: 7824 / % possible obs: 96.1 % / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.4 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1UFJ Resolution: 2.1→30.29 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 225555.4 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 86.2923 Å2 / ksol: 0.387836 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→30.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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