+Open data
-Basic information
Entry | Database: PDB / ID: 60000 | |||||||||
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Title | sperm whale myoglobin 1-nitrosopropane | |||||||||
Components | Myoglobin | |||||||||
Keywords | OXYGEN STORAGE / Myoglobin / sperm whale / 1-nitrosopropane | |||||||||
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 / Resolution: 2 Å | |||||||||
Authors | Herrera, V.E. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives. Authors: Herrera, V.E. / Charles, T.P. / Scott, T.G. / Prather, K.Y. / Nguyen, N.T. / Sohl, C.D. / 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 | 6e04.cif.gz | 52.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e04.ent.gz | 35.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e04_validation.pdf.gz | 821.2 KB | Display | wwPDB validaton report |
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Full document | 6e04_full_validation.pdf.gz | 822.5 KB | Display | |
Data in XML | 6e04_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 6e04_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/6e04 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/6e04 | HTTPS FTP |
-Related structure data
Related structure data | 6e02C 6e03C 8f9hC 8f9iC 8f9jC 8f9nC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17365.164 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P02185 |
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-Non-polymers , 5 types, 154 molecules
#2: Chemical | ChemComp-HEM / | ||||
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#3: Chemical | ChemComp-XEM / | ||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-NA / | #6: 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: 3.08 Å3/Da / Density % sol: 60.12 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 2.56-3.20 M AS, 100 mM Tris-HCl, 1 mm EDTA, pH 7.4 or 9.0. PH range: 7.4-9.0 |
-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: Mar 5, 2018 |
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: 2→45.34 Å / Num. obs: 14515 / % possible obs: 99.69 % / Redundancy: 14.2 % / Net I/σ(I): 16.78 |
Reflection shell | Resolution: 2→2.03 Å |
-Processing
Software |
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Refinement | Resolution: 2→45.34 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.038 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.135 / 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: 17.284 Å2
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Refinement step | Cycle: 1 / Resolution: 2→45.34 Å
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Refine LS restraints |
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