[English] 日本語
![](img/lk-miru.gif)
- PDB-1y85: T-To-T(High) quaternary transitions in human hemoglobin: desHIS14... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1y85 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | T-To-T(High) quaternary transitions in human hemoglobin: desHIS146beta deoxy low-salt | |||||||||
![]() |
| |||||||||
![]() | TRANSPORT PROTEIN / HEMOGLOBIN MUTANT / GLOBIN | |||||||||
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 | ![]() ![]() | |||||||||
![]() | Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. | |||||||||
![]() | ![]() Title: Crystallographic evidence for a new ensemble of ligand-induced allosteric transitions in hemoglobin: the T-to-T(high) quaternary transitions. Authors: Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. #1: ![]() Title: Structure and Oxygen Affinity of Crystalline des-His-146beta Human Hemoglobin in the T State Authors: Bettati, S. / Kwiatkowski, L.D. / Kavanaugh, J.S. / Mozzarelli, A. / Arnone, A. / Luigi-Rossi, G. / Noble, R.W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 127.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 100.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 35.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xxtSC ![]() 1xy0C ![]() 1xz5C ![]() 1xz7C ![]() 1xzuC ![]() 1xzvC ![]() 1y09C ![]() 1y0aC ![]() 1y0cC ![]() 1y0dC ![]() 1y0tC ![]() 1y0wC ![]() 1y22C ![]() 1y2zC ![]() 1y31C ![]() 1y35C ![]() 1y45C ![]() 1y46C ![]() 1y4bC ![]() 1y4fC ![]() 1y4gC ![]() 1y4pC ![]() 1y4qC ![]() 1y4rC ![]() 1y4vC ![]() 1y5fC ![]() 1y5jC ![]() 1y5kC ![]() 1y7cC ![]() 1y7dC ![]() 1y7gC ![]() 1y7zC ![]() 1y83C ![]() 1y8wC ![]() 1ydzC ![]() 1ye0C ![]() 1ye1C ![]() 1ye2C ![]() 1yenC ![]() 1yeoC ![]() 1yeqC ![]() 1yeuC ![]() 1yevC ![]() 1yg5C ![]() 1ygdC ![]() 1ygfC ![]() 1yh9C ![]() 1yheC ![]() 1yhrC ![]() 1yieC ![]() 1yihC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | the crystallographic asymmetric unit in this entry is an alpha2beta2 tetramer. the crystallographic asymmetric unit and biological unit are equivalent |
-
Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15752.052 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-145 / Source method: isolated from a natural source Details: HIS146 IS REMOVED BY ENZYMATIC DIGESTION WITH CARBOXYPEPTIDASE B Source: (natural) ![]() #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
---|---|
Crystal grow | Temperature: 298 K / Method: batch / pH: 7 Details: 10% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.00, batch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jan 20, 1996 / Details: GRAPHITE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.13→50 Å / Num. obs: 35576 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.13→2.29 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 2 / Num. unique all: 6440 / % possible all: 90.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1XXT Resolution: 2.13→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.13→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.13→2.29 Å
|