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- PDB-1y4g: T-To-T(High) quaternary transitions in human hemoglobin: betaW37G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y4g | |||||||||
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Title | T-To-T(High) quaternary transitions in human hemoglobin: betaW37G deoxy low-salt (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. #1: ![]() Title: High-Resolution Crystal Structures of Human Hemoglobin with Mutations at Tryptophan 37beta: Structural Basis for a High-Affinity T-State Authors: Kavanaugh, J.S. / Weydert, J.A. / 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 | ![]() | 126.6 KB | Display | ![]() |
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PDB format | ![]() | 100.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 26.2 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1xxtC ![]() 1xy0C ![]() 1xz5C ![]() 1xz7C ![]() 1xzuC ![]() 1xzvC ![]() 1y09C ![]() 1y0aC ![]() 1y0cC ![]() 1y0dC ![]() 1y0tC ![]() 1y0wSC ![]() 1y22C ![]() 1y2zC ![]() 1y31C ![]() 1y35C ![]() 1y45C ![]() 1y46C ![]() 1y4bC ![]() 1y4fC ![]() 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 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: 15793.104 Da / Num. of mol.: 2 / Mutation: V1M, W37G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #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: 2.56 Å3/Da / Density % sol: 51.98 % |
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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: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jul 29, 1995 / 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: 1.91→50 Å / Num. all: 44737 / Num. obs: 44737 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 1.91→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 1.4 / Num. unique all: 7177 / % possible all: 75.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Y0W Resolution: 1.91→10 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.035 / SU ML: 0.169 / Cross valid method: THROUGHOUT AND LOCALRFREE / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.158 / 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: 25.771 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→2.046 Å / Total num. of bins used: 7 /
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