+Open data
-Basic information
Entry | Database: PDB / ID: 4ood | ||||||
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Title | Structure of K42Y mutant of sperm whale myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / globin / oxygen binding | ||||||
Function / homology | Function and homology information 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 / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||
Authors | Lebioda, L. / Wang, C. / Lovelace, L.L. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of K42N and K42Y sperm whale myoglobins point to an inhibitory role of distal water in peroxidase activity. Authors: Wang, C. / 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 | 4ood.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ood.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ood.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oo/4ood ftp://data.pdbj.org/pub/pdb/validation_reports/oo/4ood | HTTPS FTP |
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-Related structure data
Related structure data | 4of9C 3ock 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: 17400.143 Da / Num. of mol.: 1 / Mutation: K42Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185 | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #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: 39.61 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2.7 M ammonium sulfate, 20 mM Tris/HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-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 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.24 Å / Num. obs: 36894 / % possible obs: 94.25 % / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 1.24→1.271 Å / % possible all: 65.15 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OCK 3ock Resolution: 1.24→24.39 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.731 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.052 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.493 Å2
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Refinement step | Cycle: LAST / Resolution: 1.24→24.39 Å
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Refine LS restraints |
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