+Open data
-Basic information
Entry | Database: PDB / ID: 2eb9 | ||||||
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Title | Crystal Structure of Cu(II)(Sal-Leu)/apo-Myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Abe, S. / Okazaki, S. / Ueno, T. / Hikage, T. / Suzuki, A. / Yamane, T. / Watanabe, Y. | ||||||
Citation | Journal: Inorg.Chem. / Year: 2007 Title: Design and Structure Analysis of Artificial Metalloproteins: Selective Coordination of His64 to Copper Complexes with Square-Planar Structure in the apo-Myoglobin Scaffold Authors: Abe, S. / Ueno, T. / Reddy, P.A.N. / Okazaki, S. / Hikage, T. / Suzuki, A. / Yamane, T. / Nakajima, 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 | 2eb9.cif.gz | 48.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2eb9.ent.gz | 32.9 KB | Display | PDB format |
PDBx/mmJSON format | 2eb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/2eb9 ftp://data.pdbj.org/pub/pdb/validation_reports/eb/2eb9 | HTTPS FTP |
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-Related structure data
Related structure data | 2eb8C 1v9qS 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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-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) / Strain (production host): TB-1 / References: UniProt: P02185 | ||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-CUS / ( | #4: Chemical | ChemComp-GOL / | #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: 2.04 Å3/Da / Density % sol: 39.82 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.37M 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: Feb 6, 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→50 Å / Num. obs: 13338 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 25.186 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 37.87 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.266 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1V9Q Resolution: 1.8→23.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.053 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.146 / 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: 25.314 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→23.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.797→1.844 Å / Total num. of bins used: 20
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