+Open data
-Basic information
Entry | Database: PDB / ID: 1spe | ||||||
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Title | SPERM WHALE NATIVE CO MYOGLOBIN AT PH 4.0, TEMP 4C | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN STORAGE / PROTEIN STRUCTURE / SPERM WHALE MYOGLOBIN / PH VALUES / CONFORMATIONAL CHANGES | ||||||
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 / Resolution: 2 Å | ||||||
Authors | Yang, F. / Phillips Jr., G.N. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Crystal structures of CO-, deoxy- and met-myoglobins at various pH values. Authors: Yang, F. / 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 | 1spe.cif.gz | 46.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1spe.ent.gz | 32.2 KB | Display | PDB format |
PDBx/mmJSON format | 1spe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1spe_validation.pdf.gz | 838.1 KB | Display | wwPDB validaton report |
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Full document | 1spe_full_validation.pdf.gz | 845.3 KB | Display | |
Data in XML | 1spe_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1spe_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sp/1spe ftp://data.pdbj.org/pub/pdb/validation_reports/sp/1spe | HTTPS FTP |
-Related structure data
Related structure data | 1vxaC 1vxbC 1vxcC 1vxdC 1vxeC 1vxfC 1vxgC 1vxhC 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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Atom site foot note | 1: TYR 151 - GLN 152 OMEGA = 227.55 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION |
-Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physeter catodon (sperm whale) / Organ: SKELETAL / Tissue: SKELETAL MUSCLE / References: UniProt: P02185 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-CMO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow | pH: 4 / Details: pH 4.0 |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Unit: %sat / Common name: ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Dec 31, 1992 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 7936 / % possible obs: 86 % / Rmerge(I) obs: 0.069 |
Reflection | *PLUS Rmerge(I) obs: 0.069 |
-Processing
Software |
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Refinement | Resolution: 2→5 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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