+Open data
-Basic information
Entry | Database: PDB / ID: 3sdn | ||||||
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Title | Structure of G65I sperm whale myoglobin mutant | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / globin fold / oxygen carrier / oxygen | ||||||
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: 1.5 Å | ||||||
Authors | Lebioda, L. / Huang, X. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Amphitrite ornata Dehaloperoxidase (DHP): Investigations of Structural Factors That Influence the Mechanism of Halophenol Dehalogenation Using "Peroxidase-like" Myoglobin Mutants and "Myoglobin-like" DHP Mutants. Authors: Du, J. / Huang, X. / Sun, S. / Wang, C. / Lebioda, L. / Dawson, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sdn.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sdn.ent.gz | 58 KB | Display | PDB format |
PDBx/mmJSON format | 3sdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sdn_validation.pdf.gz | 847.7 KB | Display | wwPDB validaton report |
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Full document | 3sdn_full_validation.pdf.gz | 851.6 KB | Display | |
Data in XML | 3sdn_validation.xml.gz | 10 KB | Display | |
Data in CIF | 3sdn_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/3sdn ftp://data.pdbj.org/pub/pdb/validation_reports/sd/3sdn | HTTPS FTP |
-Related structure data
Related structure data | 3ock 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: 17422.252 Da / Num. of mol.: 1 / Mutation: G65I 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-ACT / | ||
#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: 2.16 Å3/Da / Density % sol: 42.93 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion / pH: 6.5 Details: 34% PEG 8000, 0.3 M sodium acetate, 0.1 M PIPES, pH 6.5, VAPOR DIFFUSION, temperature 283K |
-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: Jun 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44 Å / Num. obs: 24768 / % possible obs: 87.3 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.074 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3OCK 3ock Resolution: 1.5→40.82 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.913 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 20.632 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.496→1.535 Å / Total num. of bins used: 20
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