+Open data
-Basic information
Entry | Database: PDB / ID: 5b84 | ||||||
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Title | X-ray crystal structure of met I107Y sperm whale myoglobin | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE | ||||||
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 / oxygen binding / peroxidase activity / heme binding / extracellular exosome / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å | ||||||
Authors | Yuan, H. | ||||||
Citation | Journal: Mol Biosyst / Year: 2016 Title: Distinct roles of a tyrosine-associated hydrogen-bond network in fine-tuning the structure and function of heme proteins: two cases designed for myoglobin Authors: Liao, F. / Yuan, H. / Du, K.J. / You, Y. / Gao, S.Q. / 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 | 5b84.cif.gz | 52.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b84.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 5b84.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b84_validation.pdf.gz | 798.1 KB | Display | wwPDB validaton report |
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Full document | 5b84_full_validation.pdf.gz | 800.3 KB | Display | |
Data in XML | 5b84_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 5b84_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b8/5b84 ftp://data.pdbj.org/pub/pdb/validation_reports/b8/5b84 | HTTPS FTP |
-Related structure data
Related structure data | 5b85C 4qauS 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: 17284.969 Da / Num. of mol.: 1 / Fragment: UNP residues 2-154 / Mutation: I107Y 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: 43.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30%(w/v) Polyethylene glycol 8,000, 0.1M Sodium cacodylate trihydrate pH 6.5, 0.2M Sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 19658 / % possible obs: 96.2 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.8 % / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QAU Resolution: 1.61→35.57 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.713 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.091 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.091 Å2
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Refinement step | Cycle: 1 / Resolution: 1.61→35.57 Å
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Refine LS restraints |
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