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Yorodumi- PDB-1ufj: Crystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ufj | ||||||
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Title | Crystal Structure of an Artificial Metalloprotein:Fe(III)(3,3'-Me2-salophen)/apo-A71G Myoglobin | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / myoglobin / schiff base / iron / salophen / metalloprotein / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information hydrogen peroxide mediated signaling pathway / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 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 | 1ufj.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ufj.ent.gz | 35 KB | Display | PDB format |
PDBx/mmJSON format | 1ufj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/1ufj ftp://data.pdbj.org/pub/pdb/validation_reports/uf/1ufj | HTTPS FTP |
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-Related structure data
Related structure data | 1ufpC 1j3fS 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: 17352.123 Da / Num. of mol.: 1 / Mutation: A71G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: TB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||||
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#2: Chemical | ChemComp-FE / | ||||
#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CZM / ' | #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: 2.08 Å3/Da / Density % sol: 40.82 % |
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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 FR-E / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 23, 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: 1.6→40 Å / Num. all: 19013 / Num. obs: 19013 / % possible obs: 95.7 % / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 41.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 6.8 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1J3F Resolution: 1.6→24.93 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2246955.48 / 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: 67.4581 Å2 / ksol: 0.394893 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→24.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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