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- PDB-2hbf: HIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKY... -
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Basic information
Entry | Database: PDB / ID: 2hbf | ||||||
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Title | HIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKYL ISOCYANIDE COMPLEXES | ||||||
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![]() | OXYGEN TRANSPORT | ||||||
Function / homology | ![]() nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol 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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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70 KB | Display | ![]() |
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PDB format | ![]() | 53.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 545.3 KB | Display | ![]() |
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Full document | ![]() | 559.9 KB | Display | |
Data in XML | ![]() | 10 KB | Display | |
Data in CIF | ![]() | 13.5 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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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() | ||||
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#2: Protein | Mass: 15890.198 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.03 % |
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Processing
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Refinement | Resolution: 2.2→5 Å / Rfactor Rwork: 0.179 / Rfactor obs: 0.179 / σ(F): 0 Details: REFINEMENT. THE STARTING MODEL WAS THE ETHYL ISOCYANIDE - HEMOGLOBIN COMPLEX WITH THE LIGAND REMOVED AND THE N-PROPYL ISOCYANIDE LIGAND MODELED INTO INITIAL DIFFERENCE MAP (FO-FC) ELECTRON ...Details: REFINEMENT. THE STARTING MODEL WAS THE ETHYL ISOCYANIDE - HEMOGLOBIN COMPLEX WITH THE LIGAND REMOVED AND THE N-PROPYL ISOCYANIDE LIGAND MODELED INTO INITIAL DIFFERENCE MAP (FO-FC) ELECTRON DENSITY. THE PROGRAM X-PLOR WAS USED TO ACHIEVE A FINAL CONVENTIONAL R-FACTOR OF 17.9%. THE REFINEMENT PROCESS INCLUDED SIMULATED ANNEALING FOLLOWED BY POSITION AND TEMPERATURE FACTOR REFINEMENT. AN ITERATIVE PROCESS OF MANUAL REFITTING OF SIDE CHAINS AND PLACEMENT OF WATERS WAS PERFORMED UNTIL THE R-FACTOR CONVERGED. THE WEIGHTING OF PSEUDO-ENERGY X-RAY TERM WAS ADJUSTED TO GIVE A BOND RMS OF 0.020 ANGSTROMS IN THE LAST FEW STEPS OF POSITIONAL REFINEMENT. WATERS (N=109) WERE RETAINED FROM THE STARTING STRUCTURE OF OXYHEMOGLOBIN (1HHO). 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 114 WATERS WAS REACHED. THIS WAS REDUCED TO 55 WATERS OVER THE LAST FEW REFINEMENT CYCLES BY DELETING WATERS WHICH FELL BELOW A 20% THRESHOLD. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→5 Å
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Refine LS restraints |
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