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Open data
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Basic information
Entry | Database: PDB / ID: 1lfl | ||||||
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Title | DEOXY HEMOGLOBIN (90% RELATIVE HUMIDITY) | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / T State / HUMIDITY / ENVIRONMENT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 | ![]() | ||||||
![]() | Biswal, B.K. / Vijayan, M. | ||||||
![]() | ![]() Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state. Authors: Biswal, B.K. / Vijayan, M. #1: ![]() Title: Structure of human oxyhaemoglobin at 2.1 A resolution Authors: Shaanan, B. #2: ![]() Title: The crystal structure of human deoxyhaemoglobin at 1.74 A resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R. #3: ![]() Title: A Third Quaternary Structure of Human Hemoglobin a at 1.7-Angstroms Resolution Authors: Silva, M.M. / Rogers, P.H. / Arnone, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 232.7 KB | Display | ![]() |
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PDB format | ![]() | 192.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 50 KB | Display | |
Data in CIF | ![]() | 65.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jy7C ![]() 1lfqC ![]() 1lftC ![]() 1lfvC ![]() 1lfyC ![]() 1lfzC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.2 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.7 / Details: phosphate buffer, pH 6.7, LIQUID DIFFUSION at 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Highest resolution: 2.7 Å / Num. obs: 25510 / Biso Wilson estimate: 30.7 Å2 |
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Processing
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Refinement | Resolution: 2.7→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 192934.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.6142 Å2 / ksol: 0.296282 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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