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Yorodumi- PDB-5c6y: A sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-hem... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5c6y | |||||||||||||||
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Title | A sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-heme cross-link | |||||||||||||||
Components | Myoglobin | |||||||||||||||
Keywords | METAL BINDING PROTEIN / myoglobin / METAL BINDING PROTEIN (FE) | |||||||||||||||
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: 1.793 Å | |||||||||||||||
Authors | Yuan, H. / Lin, Y.W. / Tan, X.S. | |||||||||||||||
Funding support | China, 4items
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Citation | Journal: Dalton Trans / Year: 2015 Title: How a novel tyrosine-heme cross-link fine-tunes the structure and functions of heme proteins: a direct comparitive study of L29H/F43Y myoglobin Authors: Yan, D.J. / Yuan, H. / Li, W. / Xiang, Y. / He, B. / Nie, C.M. / Wen, G.B. / Lin, Y.W. / Tan, X.S. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c6y.cif.gz | 51.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c6y.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 5c6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5c6y_validation.pdf.gz | 809.6 KB | Display | wwPDB validaton report |
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Full document | 5c6y_full_validation.pdf.gz | 813.5 KB | Display | |
Data in XML | 5c6y_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 5c6y_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/5c6y ftp://data.pdbj.org/pub/pdb/validation_reports/c6/5c6y | HTTPS FTP |
-Related structure data
Related structure data | 4lpiC 4qauS S: Starting model for refinement C: citing same article (ref.) |
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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: 17407.137 Da / Num. of mol.: 1 / Mutation: L29H/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: 2.2 Å3/Da / Density % sol: 44.13 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Sodium acetate trihydrate,0.1 M Sodium cacodylate trihydrate pH 6.5,30% w/v Polyethylene glycol 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.988 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.988 Å / Relative weight: 1 |
Reflection | Resolution: 1.793→50 Å / Num. obs: 14678 / % possible obs: 99.7 % / Redundancy: 13 % / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.793→1.83 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 12.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QAU Resolution: 1.793→41.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.724 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.106 / 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: 22.367 Å2
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Refinement step | Cycle: 1 / Resolution: 1.793→41.26 Å
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Refine LS restraints |
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