+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jy7 | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF HUMAN METHEMOGLOBIN. THE VARIATION OF A THEME | ||||||
![]() |
| ||||||
![]() | OXYGEN STORAGE/TRANSPORT / HUMAN METHEMOGLOBIN / OXYGEN TRANSPORT / 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 methaemoglobin: The variation of a theme Authors: Biswal, B.K. / Vijayan, M. #2: ![]() Title: Structure of human oxyhaemoglobin at 2.1 A resolution Authors: Shaanan, B. #3: ![]() Title: The Crystal Structure of Human Deoxyhemoglobin at 1.74 Angstroms Resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R. #4: ![]() Title: A third quaternary structure of human hemoglobin A at 1.7-A resolution Authors: Silva, M.M. / Rogers, P.H. / Arnone, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 307.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 260.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.7 MB | Display | |
Data in XML | ![]() | 42.9 KB | Display | |
Data in CIF | ![]() | 59 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lflC ![]() 1lfqC ![]() 1lftC ![]() 1lfvC ![]() 1lfyC ![]() 1lfzC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
3 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-HEM / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 6.7 Details: PEG 4000, Sodium potassium phosphate, pH 6.7, LIQUID DIFFUSION at 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→10 Å / Num. obs: 84268 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.108 |
Reflection shell | Resolution: 3.2→3.3 Å / Rmerge(I) obs: 0.379 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: HUMAN OXYHEMOGLOBIN Resolution: 3.2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 158735.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9737 Å2 / ksol: 0.20873 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 85 Å2
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.39 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
| ||||||||||||||||||||
Xplor file |
|