[English] 日本語
Yorodumi- PDB-1ymb: HIGH RESOLUTION STUDY OF THE THREE-DIMENSIONAL STRUCTURE OF HORSE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ymb | ||||||
---|---|---|---|---|---|---|---|
Title | HIGH RESOLUTION STUDY OF THE THREE-DIMENSIONAL STRUCTURE OF HORSE HEART METMYOGLOBIN | ||||||
Components | METMYOGLOBIN | ||||||
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: 1.9 Å | ||||||
Authors | Evans, S.V. / Brayer, G.D. | ||||||
Citation | 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. #1: Journal: J.Biol.Chem. / Year: 1988 Title: Horse Heart Metmyoglobin: A 2.8 Angstrom Resolution Three-Dimensional Structure Determination Authors: Evans, S.V. / Brayer, G.D. #2: 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ymb.cif.gz | 46.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ymb.ent.gz | 33 KB | Display | PDB format |
PDBx/mmJSON format | 1ymb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ymb_validation.pdf.gz | 814.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ymb_full_validation.pdf.gz | 826.7 KB | Display | |
Data in XML | 1ymb_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1ymb_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1ymb ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1ymb | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.88 Å3/Da / Density % sol: 34.53 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 7 / Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å |
---|
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor obs: 0.155 / Highest resolution: 1.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor obs: 0.155 / Lowest resolution: 6 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|