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- PDB-1ygd: T-To-T(High) quaternary transitions in human hemoglobin: betaW37E... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ygd | ||||||
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Title | T-To-T(High) quaternary transitions in human hemoglobin: betaW37E alpha zinc beta oxy (10 TEST SETS) | ||||||
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![]() | 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.3 KB | Display | ![]() |
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PDB format | ![]() | 100.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 36.2 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 ![]() 1y4pSC ![]() 1y4qC ![]() 1y4rC ![]() 1y4vC ![]() 1y5fC ![]() 1y5jC ![]() 1y5kC ![]() 1y7cC ![]() 1y7dC ![]() 1y7gC ![]() 1y7zC ![]() 1y83C ![]() 1y85C ![]() 1y8wC ![]() 1ydzC ![]() 1ye0C ![]() 1ye1C ![]() 1ye2C ![]() 1yenC ![]() 1yeoC ![]() 1yeqC ![]() 1yeuC ![]() 1yevC ![]() 1yg5C ![]() 1ygfC ![]() 1yh9C ![]() 1yheC ![]() 1yhrC ![]() 1yieC ![]() 1yihC C: citing same article ( S: Starting model for refinement |
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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 biological unit are equivalent |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15865.167 Da / Num. of mol.: 2 / Mutation: V1M, W37E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 4 types, 181 molecules ![](data/chem/img/ZNH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Details: 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, PH 7.0, BATCH, TEMPERATURE 298K, 1 ATM N2. EXPOSING DEOXY CRYSTAL TO LIGAND: A ...Details: 10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, PH 7.0, BATCH, TEMPERATURE 298K, 1 ATM N2. EXPOSING DEOXY CRYSTAL TO LIGAND: A DEOXY CRYSTAL WAS SOAKED (UNDER 1 ATM NITROGEN) IN SUBSTITUTE MOTHER LIQUOR CONTAINING 13% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE. THE CRYSTAL WAS THEN EXPOSED TO AIR AT 298K AND DATA WAS COLLECTED AT 298K. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Dec 23, 1997 / 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: 2.73→50 Å / Num. obs: 17254 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.73→2.94 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3138 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Y4P Resolution: 2.73→10 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.842 / SU B: 9.009 / SU ML: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.424 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: A and C chain hemes contain zinc instead of iron
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.865 Å2
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Refinement step | Cycle: LAST / Resolution: 2.73→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.73→2.931 Å / Total num. of bins used: 7 /
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