+Open data
-Basic information
Entry | Database: PDB / ID: 4qau | ||||||
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Title | Crystal structure of F43Y mutant of sperm whale myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / alpha helix boundle / F43Y mutant | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å | ||||||
Authors | Lin, Y. / Tan, X. / Li, W. | ||||||
Citation | Journal: Chembiochem / Year: 2015 Title: A Novel Tyrosine-Heme C-O Covalent Linkage in F43Y Myoglobin: A New Post-translational Modification of Heme Proteins Authors: Yan, D.-J. / Li, W. / Xiang, Y. / Wen, G.-B. / Lin, Y.-W. / Tan, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qau.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qau.ent.gz | 34.4 KB | Display | PDB format |
PDBx/mmJSON format | 4qau.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/4qau ftp://data.pdbj.org/pub/pdb/validation_reports/qa/4qau | HTTPS FTP |
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-Related structure data
Related structure data | 4it8S 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: 17382.148 Da / Num. of mol.: 1 / Mutation: F43Y 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: 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: 2.19 Å3/Da / Density % sol: 43.75 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate, 30% w/v Polyethylene glycol 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2013 / Details: mirrors | |||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.5967→30.78 Å / Num. obs: 20569 / % possible obs: 10.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.9 % / Rmerge(I) obs: 0.357 / Rsym value: 0.077 / Net I/σ(I): 26.9 | |||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4it8 Resolution: 1.597→30.774 Å / SU ML: 0.33 / σ(F): 0.13 / Phase error: 18.11 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.065 Å2 / ksol: 0.398 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.597→30.774 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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