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- PDB-2mya: HIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKY... -
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Basic information
Entry | Database: PDB / ID: 2mya | ||||||
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Title | HIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKYL ISOCYANIDE COMPLEXES | ||||||
![]() | MYOGLOBIN (ETHYL ISOCYANIDE) | ||||||
![]() | OXYGEN STORAGE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Johnson, K.A. / Olson, J.S. / Phillips Jr., G.N. | ||||||
![]() | Journal: Thesis / Year: 1993 Title: High Resolution X-Ray Structures of Myoglobin-and Hemoglobin-Alkyl Isocyanide Complexes Authors: Johnson, K.A. #1: ![]() Title: Structure of Myoglobin-Ethyl Isocyanide: Histidine as a Swinging Door for Ligand Entry Authors: Johnson, K.A. / Olson, J.S. / Phillips Jr., G.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 47.4 KB | Display | ![]() |
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PDB format | ![]() | 33.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 484.8 KB | Display | ![]() |
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Full document | ![]() | 488.5 KB | Display | |
Data in XML | ![]() | 5.8 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17234.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-HEM / |
#4: Chemical | ChemComp-ENC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.88 % |
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Processing
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Refinement | Resolution: 1.8→5 Å / Rfactor Rwork: 0.178 / Rfactor obs: 0.178 / σ(F): 0 Details: WATERS WERE RETAINED FROM THE STARTING STRUCTURE OF OXYMYOGLOBIN (PROTEIN DATA BANK ENTRY 1MBO). ADDITIONAL WATERS WERE ADDED IF THEY LAY IN 3.5 - 4.O SIGMA PEAKS IN FO-FC ELECTRON DENSITY ...Details: WATERS WERE RETAINED FROM THE STARTING STRUCTURE OF OXYMYOGLOBIN (PROTEIN DATA BANK ENTRY 1MBO). ADDITIONAL WATERS WERE ADDED IF THEY LAY IN 3.5 - 4.O SIGMA PEAKS IN FO-FC ELECTRON DENSITY MAPS AND 1 SIGMA PEAKS IN 2FO-FC MAPS. CONCURRENTLY, A WATER WOULD BE DELETED IF ITS OCCUPANCY (Q) AND TEMPERATURE FACTOR (B) COMBINED TO MAKE THE VALUE Q*EXP(-B/36)*100% FALL BELOW 10%. A PEAK NUMBER OF 340 WATERS WAS REACHED. THIS WAS REDUCED TO 162 WATERS OVER THE LAST FEW REFINEMENT CYCLES BY DELETING WATERS WHICH FELL BELOW A 20% THRESHOLD. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→5 Å
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Refine LS restraints |
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