+Open data
-Basic information
Entry | Database: PDB / ID: 2oh9 | ||||||
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Title | Myoglobin cavity mutant V68W | ||||||
Components | Myoglobin | ||||||
Keywords | OXYGEN STORAGE/TRANSPORT / MYOGLOBIN / LIGAND ENTRY AND EXIT PATHWAYS / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Phillips Jr., G.N. / Li, T. / Brucker, E.A. / Soman, J. / Olson, J.S. | ||||||
Citation | Journal: Iubmb Life / Year: 2007 Title: Ligand pathways in myoglobin: A review of trp cavity mutations. Authors: Olson, J.S. / Soman, J. / Phillips, G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oh9.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oh9.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oh9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oh9_validation.pdf.gz | 810.1 KB | Display | wwPDB validaton report |
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Full document | 2oh9_full_validation.pdf.gz | 810.6 KB | Display | |
Data in XML | 2oh9_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 2oh9_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/2oh9 ftp://data.pdbj.org/pub/pdb/validation_reports/oh/2oh9 | HTTPS FTP |
-Related 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: 17452.240 Da / Num. of mol.: 1 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-resistent TB1 / References: UniProt: P02185 | ||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #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: 3.18 Å3/Da / Density % sol: 61.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: PROTEIN SOLUTION (20 MG/ML PROTEIN, 0.020 M TRIS-HCL, pH 9.0), MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (2.8 M AMMONIUM SULPHATE, 0.050 M TRIS-HCL, pH9.0), vapor diffusion, hanging drop, ...Details: PROTEIN SOLUTION (20 MG/ML PROTEIN, 0.020 M TRIS-HCL, pH 9.0), MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (2.8 M AMMONIUM SULPHATE, 0.050 M TRIS-HCL, pH9.0), vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Monochromator: FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.89 Å / Num. all: 24077 / Num. obs: 24077 / Observed criterion σ(F): 0 / Biso Wilson estimate: 21.7 Å2 / Limit h max: 46 / Limit h min: 0 / Limit k max: 46 / Limit k min: 0 / Limit l max: 26 / Limit l min: 0 / Observed criterion F max: 535784.92 / Observed criterion F min: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.89 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 63.8528 Å2 / ksol: 0.37372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 62.69 Å2 / Biso mean: 23.66 Å2 / Biso min: 11.59 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→45.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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