+Open data
-Basic information
Entry | Database: PDB / ID: 5iks | ||||||
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Title | Wild-type sperm whale myoglobin with a Fe-phenyl moiety | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Bioorganometallic / Heme / Myoglobin / Sigma-aryl / Iron-carbon / Hydrazine / Arylhydrazine / Phenylhydrazine / Tolylhydrazine / 3-methylphenylhydrazine / para-chlorophenylhdrazine / 4-chlorophenylhydrazine | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Model details | This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine. | ||||||
Authors | Wang, B. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Inorg. Biochem. / Year: 2016 Title: Organometallic myoglobins: Formation of Fe-carbon bonds and distal pocket effects on aryl ligand conformations. Authors: Wang, B. / Thomas, L.M. / Richter-Addo, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5iks.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iks.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 5iks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iks_validation.pdf.gz | 861.3 KB | Display | wwPDB validaton report |
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Full document | 5iks_full_validation.pdf.gz | 864.3 KB | Display | |
Data in XML | 5iks_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 5iks_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5iks ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5iks | HTTPS FTP |
-Related structure data
Related structure data | 5ileC 5ilmC 5ilpC 5ilrC 2mbwS 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: 17048.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-6CO / [ |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-GOL / |
#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: 1.9 Å3/Da / Density % sol: 35.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1 M Tris-HCl, pH 7.4, 1mM EDTA, 2.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 24, 2014 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→50 Å / Num. obs: 10468 / % possible obs: 97.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.032 / Net I/av σ(I): 37.234 / Net I/σ(I): 18.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2MBW Resolution: 1.87→33.28 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.877 / SU B: 4.05 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.041 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 59.61 Å2 / Biso mean: 20.191 Å2 / Biso min: 9.89 Å2
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Refinement step | Cycle: final / Resolution: 1.87→33.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.869→1.918 Å / Total num. of bins used: 20
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