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Yorodumi- PDB-1mbc: X-RAY STRUCTURE AND REFINEMENT OF CARBON-MONOXY (FE II)-MYOGLOBIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mbc | ||||||
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Title | X-RAY STRUCTURE AND REFINEMENT OF CARBON-MONOXY (FE II)-MYOGLOBIN AT 1.5 ANGSTROMS RESOLUTION | ||||||
Components | MYOGLOBIN | ||||||
Keywords | 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 / Resolution: 1.5 Å | ||||||
Authors | Kuriyan, J. / Petsko, G.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1986 Title: X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 A resolution. Authors: Kuriyan, J. / Wilz, S. / Karplus, M. / Petsko, G.A. #1: Journal: Proteins / Year: 1987 Title: Estimation of Uncertainties in X-Ray Refinement Results by Use of Perturbed Structures Authors: Kuriyan, J. / Karplus, M. / Petsko, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mbc.cif.gz | 47.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mbc.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 1mbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mbc_validation.pdf.gz | 486.2 KB | Display | wwPDB validaton report |
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Full document | 1mbc_full_validation.pdf.gz | 498.1 KB | Display | |
Data in XML | 1mbc_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1mbc_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/1mbc ftp://data.pdbj.org/pub/pdb/validation_reports/mb/1mbc | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SEE REMARK 4. |
-Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Physeter catodon (sperm whale) / 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: 1.92 Å3/Da / Density % sol: 35.8 % |
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Crystal grow | *PLUS Method: unknown |
-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Num. obs: 10448 / Num. measured all: 18520 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.171 / Highest resolution: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.5 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Highest resolution: 2.5 Å / Rfactor obs: 0.171 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_mcbond_it / Dev ideal: 0.9 |