+Open data
-Basic information
Entry | Database: PDB / ID: 5ojb | ||||||
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Title | Structure of MbQ NMH | ||||||
Components | Myoglobin | ||||||
Keywords | OXIDOREDUCTASE / myoglobin / NMH / N-methylhistidine / heme | ||||||
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: 1.543 Å | ||||||
Authors | Hayashi, T. / Pott, M. / Mori, T. / Mittl, P. / Green, A. / Hivert, D. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: A Noncanonical Proximal Heme Ligand Affords an Efficient Peroxidase in a Globin Fold. Authors: Pott, M. / Hayashi, T. / Mori, T. / Mittl, P.R.E. / Green, A.P. / Hilvert, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ojb.cif.gz | 50.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ojb.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ojb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ojb_validation.pdf.gz | 803.7 KB | Display | wwPDB validaton report |
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Full document | 5ojb_full_validation.pdf.gz | 804.5 KB | Display | |
Data in XML | 5ojb_validation.xml.gz | 9.2 KB | Display | |
Data in CIF | 5ojb_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/5ojb ftp://data.pdbj.org/pub/pdb/validation_reports/oj/5ojb | HTTPS FTP |
-Related structure data
Related structure data | 5oj9SC 5ojaC 5ojcC 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
#1: Protein | Mass: 18379.178 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) / References: UniProt: P02185 |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-IMD / |
#4: 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: 2.59 Å3/Da / Density % sol: 52.48 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M SPG (pH 7.0), 30% PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. obs: 54004 / % possible obs: 99.4 % / Redundancy: 5.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.83 |
Reflection shell | Resolution: 1.54→1.64 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.285 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 8534 / CC1/2: 0.552 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OJ9 Resolution: 1.543→45.567 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 26.36
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.543→45.567 Å
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Refine LS restraints |
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LS refinement shell |
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