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Yorodumi- PDB-2ef2: Crystal Structure of an Artificial Metalloprotein:Rh(Phebox-Ph)/a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ef2 | ||||||
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Title | Crystal Structure of an Artificial Metalloprotein:Rh(Phebox-Ph)/apo-A71G Myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Abe, S. / Satake, Y. / Okazaki, S. / Ueno, T. / Hikage, T. / Suzuki, A. / Yamane, T. / Nakajima, H. / Watanabe, Y. | ||||||
Citation | Journal: ORGANOMETALLICS / Year: 2007 Title: Incorporation of a Phebox Rhodium Complex into apo-Myoglobin Affords a Stable Organometallic Protein Showing Unprecedented Arrangement of the Complex in the Cavity Authors: Satake, Y. / Abe, S. / Okazaki, S. / Ban, N. / Hikage, T. / Ueno, T. / Nakajima, H. / Suzuki, A. / Yamane, T. / Nishiyama, H. / Watanabe, Y. | ||||||
History |
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Remark 650 | HELIX Determination method: Author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ef2.cif.gz | 48 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ef2.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 2ef2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ef2_validation.pdf.gz | 810.9 KB | Display | wwPDB validaton report |
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Full document | 2ef2_full_validation.pdf.gz | 812.3 KB | Display | |
Data in XML | 2ef2_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 2ef2_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2ef2 ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2ef2 | HTTPS FTP |
-Related structure data
Related structure data | 1vfjS 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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-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: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P02185 | ||||
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#2: Chemical | #3: Chemical | ChemComp-RHX / [ | #4: 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: 40.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.35M Sodium, Pottasium Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 26, 2006 |
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: 1.8→80 Å / Num. obs: 13570 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 22.865 Å2 / Rmerge(I) obs: 0.057 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.293 / % possible all: 94.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VFJ Resolution: 1.8→21.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.709 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→21.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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