+Open data
-Basic information
Entry | Database: PDB / ID: 5utc | ||||||
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Title | Deoxy form of sperm whale myoglobin V68A/I107Y | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Heme / Myoglobin / Nitrite / Nitrosyl / Nitric oxide / deoxy | ||||||
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: 1.8 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: Biochemistry / Year: 2018 Title: Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets. Authors: Wang, B. / Shi, Y. / Tejero, J. / Powell, S.M. / Thomas, L.M. / Gladwin, M.T. / Shiva, S. / Zhang, Y. / 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 | 5utc.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5utc.ent.gz | 33.5 KB | Display | PDB format |
PDBx/mmJSON format | 5utc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5utc_validation.pdf.gz | 853.8 KB | Display | wwPDB validaton report |
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Full document | 5utc_full_validation.pdf.gz | 856.9 KB | Display | |
Data in XML | 5utc_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 5utc_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/5utc ftp://data.pdbj.org/pub/pdb/validation_reports/ut/5utc | HTTPS FTP |
-Related structure data
Related structure data | 5ut7C 5ut8C 5ut9C 5utaC 5utbC 5utdC 5vznC 5vzoC 5vzpC 5vzqC 6cf0C 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: 17387.127 Da / Num. of mol.: 1 / Mutation: V68A, I107Y 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: 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: 1.9 Å3/Da / Density % sol: 35.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl, 1 mM EDTA, pH 7.4 2.56 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: Nov 10, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→31 Å / Num. obs: 12004 / % possible obs: 99 % / Redundancy: 3 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.031 / Rrim(I) all: 0.056 / Χ2: 4.048 / Net I/σ(I): 39.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→26.37 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 3.176 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.16 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: 65.01 Å2 / Biso mean: 23.633 Å2 / Biso min: 11.33 Å2
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Refinement step | Cycle: final / Resolution: 1.8→26.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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