+Open data
-Basic information
Entry | Database: PDB / ID: 3ogb | ||||||
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Title | Sperm whale myoglobin mutant H64W deoxy-form | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN TRANSPORT / Myoglobin / ligand migration pathways / oxygen storage | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Birukou, I. / Soman, J. / Olson, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Blocking the gate to ligand entry in human hemoglobin. Authors: Birukou, I. / Soman, J. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ogb.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ogb.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ogb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ogb_validation.pdf.gz | 816 KB | Display | wwPDB validaton report |
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Full document | 3ogb_full_validation.pdf.gz | 817.5 KB | Display | |
Data in XML | 3ogb_validation.xml.gz | 12 KB | Display | |
Data in CIF | 3ogb_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/3ogb ftp://data.pdbj.org/pub/pdb/validation_reports/og/3ogb | HTTPS FTP |
-Related structure data
Related structure data | 3nl7C 3nmlSC 3nmmC 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: 17413.225 Da / Num. of mol.: 1 / Mutation: H65W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): PHAGE RESISTANT TB1 / References: UniProt: P02185 | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | ChemComp-SO4 / #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: 2.34 Å3/Da / Density % sol: 47.36 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 9 Details: Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ...Details: Solution of MB (carbonmonoxy-form) (20mg/ml protein in 0.02M TRIS-HCl pH 9.0) mixed with mother liquor (3.2M ammonium sulphate, 0.05M TRIS-HCl, pH 9.0) for final concentrations of 2.5M ammonium sulphate to obtain crystals of MBCO. MBCO crystals were oxidyzed by excess of potassium ferricyanide, washed in mother liquor and reduced under anaerobic conditions with sodium dithionite, SMALL TUBES, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 23, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→23.57 Å / Num. obs: 21466 / % possible obs: 96.6 % / Redundancy: 3.65 % / Rmerge(I) obs: 0.043 / Χ2: 0.95 / Net I/σ(I): 15.5 / Scaling rejects: 695 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 3NML Resolution: 1.6→23.565 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.122 Å2 / ksol: 0.435 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.49 Å2 / Biso mean: 20.7404 Å2 / Biso min: 9.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23.565 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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