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- PDB-1yhr: T-To-T(High) quaternary transitions in human hemoglobin: HbA OXY ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yhr | ||||||
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Title | T-To-T(High) quaternary transitions in human hemoglobin: HbA OXY (10.0MM IHP, 20% PEG) (10 test sets) | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / GLOBIN / 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 | ![]() ![]() | ||||||
![]() | 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. | ||||||
History |
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Remark 600 | HETEROGEN AN IHP MOLECULE WAS NOT ADDED TO THE MODEL SINCE NO SIGNIFICANT ELECTRON DENSITY WAS ...HETEROGEN AN IHP MOLECULE WAS NOT ADDED TO THE MODEL SINCE NO SIGNIFICANT ELECTRON DENSITY WAS FOUND AT ITS BINDING SITE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.4 KB | Display | ![]() |
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PDB format | ![]() | 101.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xxtC ![]() 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 ![]() 1y85C ![]() 1y8wC ![]() 1ydzC ![]() 1ye0C ![]() 1ye1C ![]() 1ye2C ![]() 1yenC ![]() 1yeoC ![]() 1yeqC ![]() 1yeuC ![]() 1yevC ![]() 1yg5C ![]() 1ygdC ![]() 1ygfC ![]() 1yh9C ![]() 1yheC ![]() 1yieC ![]() 1yihC ![]() 1rq3S S: Starting model for refinement 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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Unit cell |
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Details | the crystallographic asymmetric unit in this entry is an alpha2beta2 tetramer. the crystallographic asymmetric unit and the biological unit are equivalent |
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Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-OXY / #4: Chemical | ChemComp-HEM / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.95 % Description: EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM ...Description: EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 10.0 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K. |
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Crystal grow | Temperature: 298 K / pH: 7 Details: 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.0, batch, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 169 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 26, 2001 / Details: OSMIC MIRRORS |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30.429 Å / Num. obs: 18673 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.6→2.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3549 / % possible all: 89 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RQ3 Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.84 / SU B: 19.534 / SU ML: 0.413 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.361 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.793 Å / Total num. of bins used: 7 /
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