+Open data
-Basic information
Entry | Database: PDB / ID: 1ymc | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF CYANOMET-SULFMYOGLOBIN C | ||||||
Components | CYANOMET-SULFMYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
Function / homology | Function and homology information nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / oxygen binding / peroxidase activity / heme binding ...nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / 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 | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Evans, S.V. / Brayer, G.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Three-dimensional structure of cyanomet-sulfmyoglobin C. Authors: Evans, S.V. / Sishta, B.P. / Mauk, A.G. / Brayer, G.D. #1: Journal: J.Mol.Biol. / Year: 1990 Title: High-Resolution Study of the Three-Dimensional Structure of Horse Heart Metmyoglobin Authors: Evans, S.V. / Brayer, G.D. #2: Journal: J.Biol.Chem. / Year: 1988 Title: Horse Heart Metmyoglobin: A 2.8-Angstroms Resolution Three-Dimensional Structure Determination Authors: Evans, S.V. / Brayer, G.D. #3: Journal: J.Mol.Biol. / Year: 1987 Title: Crystallization and Preliminary Diffraction Data for Horse Heart Metmyoglobin Authors: Sherwood, C. / Mauk, A.G. / Brayer, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ymc.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ymc.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 1ymc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ymc_validation.pdf.gz | 825.6 KB | Display | wwPDB validaton report |
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Full document | 1ymc_full_validation.pdf.gz | 848.3 KB | Display | |
Data in XML | 1ymc_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1ymc_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ymc ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ymc | 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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-Components
#1: Protein | Mass: 16983.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P68082 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CYN / |
#4: Chemical | ChemComp-CLN / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.28 % | |||||||||||||||
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Crystal grow | *PLUS Method: batch method / Details: can also be done with hanging drop vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. obs: 7946 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 5369 / σ(F): 2 / Rfactor obs: 0.129 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.06 |