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- PDB-1y09: T-to-T(High) Quaternary Transitions in Human Hemoglobin: alphaN97... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y09 | ||||||
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Title | T-to-T(High) Quaternary Transitions in Human Hemoglobin: alphaN97A deoxy low-salt | ||||||
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![]() | TRANSPORT PROTEIN / hemoglobin mutant / globin | ||||||
Function / homology | ![]() nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / carbon dioxide transport / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.9 KB | Display | ![]() |
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PDB format | ![]() | 100.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 26.7 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xxtC ![]() 1xy0C ![]() 1xz5C ![]() 1xz7C ![]() 1xzuC ![]() 1xzvC ![]() 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 ![]() 1yhrC ![]() 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 asymmetric unit in this entry is an alpha2beta2 tetramer. the biological unit is an alpha2beta2 tetramer. the crystallographic asymmetric unit and the biological unit are equivalent |
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Components
#1: Protein | Mass: 15139.394 Da / Num. of mol.: 2 / Mutation: V1M, N97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / 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: 2.57 Å3/Da / Density % sol: 52.06 % |
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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 7.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2004 / 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: 2.25→50 Å / Num. all: 26928 / Num. obs: 26928 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.25→2.43 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4527 / % possible all: 72.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1RQ3 Resolution: 2.25→10 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 9.301 / SU ML: 0.229 / Cross valid method: THROUGHOUT and local R-free analysis / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.231 / 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: 32.639 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.42 Å / Total num. of bins used: 7 /
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