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Yorodumi- PDB-3u3e: Complex of Wild Type Myoglobin with Phenol in its Proximal Cavity -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u3e | ||||||
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Title | Complex of Wild Type Myoglobin with Phenol in its Proximal Cavity | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Heme containing / Phenol Binding | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Celeste, L.R. / Lebioda, L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: Complex of myoglobin with phenol bound in a proximal cavity. Authors: Huang, X. / Wang, C. / Celeste, L.R. / Lovelace, L.L. / Sun, S. / Dawson, J.H. / Lebioda, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u3e.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u3e.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 3u3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u3e_validation.pdf.gz | 846.5 KB | Display | wwPDB validaton report |
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Full document | 3u3e_full_validation.pdf.gz | 851.1 KB | Display | |
Data in XML | 3u3e_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 3u3e_validation.cif.gz | 17.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/3u3e ftp://data.pdbj.org/pub/pdb/validation_reports/u3/3u3e | HTTPS FTP |
-Related 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) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-IPH / | ||
#4: Chemical | ChemComp-SO4 / #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: 3.09 Å3/Da / Density % sol: 60.16 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 20mM Tris pH 9.0, 1mM EDTA, 2.6M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. all: 64348 / Num. obs: 64348 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.21→1.23 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 9.1 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→31.947 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.841 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0345 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.21→31.947 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.209→1.24 Å / Total num. of bins used: 20
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