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Yorodumi- PDB-1u7r: Crystal structure of Native Sperm Whale myoglobin from low ionic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1u7r | ||||||
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Title | Crystal structure of Native Sperm Whale myoglobin from low ionic strength enviroment (Form2 ) | ||||||
Components | Myoglobin | ||||||
Keywords | TRANSPORT PROTEIN / Sperm Whale myoglobin / Low ionic strength | ||||||
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 / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Physeter catodon (sperm whale) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Zhang, W. / Phillips Jr., G.N. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments. Authors: Kondrashov, D.A. / Zhang, W. / Aranda, R. / Stec, B. / Phillips Jr., G.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u7r.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u7r.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 1u7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/1u7r ftp://data.pdbj.org/pub/pdb/validation_reports/u7/1u7r | HTTPS FTP |
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-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: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Tissue: skeleton / 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: 1.83 Å3/Da / Density % sol: 32.8 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 50mM imidazole, pH 7 with 16% PEG3550, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→40 Å / Num. all: 53703 / Num. obs: 53703 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1000 / Rmerge(I) obs: 0.039 |
Reflection shell | Resolution: 1.15→1.19 Å / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.039 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→40 Å / Num. parameters: 13055 / Num. restraintsaints: 16112 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1413 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.19 Å
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