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Yorodumi- PDB-1y5f: T-To-T(High) quaternary transitions in human hemoglobin: betaL96A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y5f | ||||||
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Title | T-To-T(High) quaternary transitions in human hemoglobin: betaL96A deoxy low-salt (1 test set) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / HEMOGLOBIN MUTANT / GLOBIN | ||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / regulation of blood pressure / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. | ||||||
Citation | Journal: Biochemistry / Year: 2005 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y5f.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y5f.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 1y5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1y5f_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1y5f_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1y5f_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 1y5f_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/1y5f ftp://data.pdbj.org/pub/pdb/validation_reports/y5/1y5f | HTTPS FTP |
-Related structure data
Related structure data | 1xxtC 1xy0C 1xz5C 1xz7C 1xzuC 1xzvC 1y09C 1y0aC 1y0cC 1y0dC 1y0tSC 1y0wC 1y22C 1y2zC 1y31C 1y35C 1y45C 1y46C 1y4bC 1y4fC 1y4gC 1y4pC 1y4qC 1y4rC 1y4vC 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | the crystallographic asymmteric unit in this entry is an alpha2beta2 tetramer. the crystallographic asymmetric unit and the biological unit are equivalent |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P69905 #2: Protein | Mass: 15880.185 Da / Num. of mol.: 2 / Mutation: V1M, L96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.92 % |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jul 3, 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: 2.14→50 Å / Num. all: 35049 / Num. obs: 35049 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.14→2.31 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.206 / Mean I/σ(I) obs: 2.5 / Num. unique all: 6371 / % possible all: 90.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Y0T Resolution: 2.14→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 24.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.14→2.31 Å
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