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Yorodumi- PDB-1yma: STRUCTURAL CHARACTERIZATION OF HEME LIGATION IN THE HIS64-->TYR V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yma | ||||||
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Title | STRUCTURAL CHARACTERIZATION OF HEME LIGATION IN THE HIS64-->TYR VARIANT OF MYOGLOBIN | ||||||
Components | MYOGLOBIN | ||||||
Keywords | OXYGEN TRANSPORT | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Maurus, R. / Brayer, G.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Structural characterization of heme ligation in the His64-->Tyr variant of myoglobin. Authors: Maurus, R. / Bogumil, R. / Luo, Y. / Tang, H.L. / Smith, M. / 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 | 1yma.cif.gz | 45.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yma.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yma.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yma_validation.pdf.gz | 805.6 KB | Display | wwPDB validaton report |
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Full document | 1yma_full_validation.pdf.gz | 814.9 KB | Display | |
Data in XML | 1yma_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1yma_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1yma ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1yma | 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: 17008.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Organ: HEART / References: UniProt: P68082 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.32 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 3453 / Observed criterion σ(F): 2 / Num. measured all: 22024 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→8 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 0.024 |