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- PDB-1j3f: Crystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j3f | ||||||
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Title | Crystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me2-salophen)/apo-A71G Myoglobin | ||||||
![]() | Myoglobin | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / myoglobin / asymmetric catalysis / crystal / Schiff bases / chromium / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Koshiyama, T. / Kono, M. / Ohashi, M. / Ueno, T. / Suzuki, A. / Yamane, T. / Watanabe, Y. | ||||||
![]() | ![]() Title: Coordinated Design of Cofactor and Active Site Structures in Development of New Protein Catalysts Authors: Ueno, T. / Koshiyama, T. / Ohashi, M. / Kondo, K. / Kono, M. / Suzuki, A. / Yamane, T. / Watanabe, Y. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.9 KB | Display | ![]() |
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PDB format | ![]() | 35.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 787.1 KB | Display | ![]() |
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Full document | ![]() | 787.9 KB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 16.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v9qC ![]() 1bvcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-CR / | ||||
#3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-CZM / ' | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.72 Å3/Da / Density % sol: 28.08 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: sodium, potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 31, 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: 1.45→40 Å / Num. all: 26654 / Num. obs: 26426 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 40.6 |
Reflection shell | Resolution: 1.45→1.5 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.9 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BVC Resolution: 1.45→30.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1798486.43 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.11 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→30.26 Å
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Refine LS restraints |
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Xplor file |
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