+Open data
-Basic information
Entry | Database: PDB / ID: 600 | ||||||
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Title | WT swMb-MeNO | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE / Myoglobin / Nitrosomethane | ||||||
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 / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 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 | 6e02.cif.gz | 57.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e02.ent.gz | 39 KB | Display | PDB format |
PDBx/mmJSON format | 6e02.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/6e02 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/6e02 | HTTPS FTP |
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-Related structure data
Related structure data | 6e03C 6e04C 8f9hC 8f9iC 8f9jC 8f9nC 5ileS 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 on special symmetry positions |
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-Components
#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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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #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: 3.08 Å3/Da / Density % sol: 60.01 % |
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Crystal grow | Temperature: 298 K / Method: evaporation 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: Nov 22, 2017 |
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: 1.76→45.33 Å / Num. obs: 21127 / % possible obs: 99.89 % / Redundancy: 7.5 % / Net I/σ(I): 36.21 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 7.48 % / Rmerge(I) obs: 0.174 / Num. unique obs: 2083 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ile Resolution: 1.76→45.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.491 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.087 / 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: 13.58 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→45.33 Å
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Refine LS restraints |
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