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Yorodumi- PDB-1y8w: T-To-T(High) quaternary transitions in human hemoglobin: alphaR92... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y8w | ||||||
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Title | T-To-T(High) quaternary transitions in human hemoglobin: alphaR92A oxy (2mM IHP, 20% PEG) (10 test sets) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / HEMOGLOBIN MUTANT / GLOBIN | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin 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 / 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 / platelet aggregation / oxygen binding / regulation of blood pressure / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 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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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y8w.cif.gz | 128.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y8w.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 1y8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y8w ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y8w | HTTPS FTP |
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-Related structure data
Related structure data | 1xxtC 1xy0C 1xz5C 1xz7SC 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 1ydzC 1ye0C 1ye1C 1ye2C 1yenC 1yeoC 1yeqC 1yeuC 1yevC 1yg5C 1ygdC 1ygfC 1yh9C 1yheC 1yhrC 1yieC 1yihC C: citing same article (ref.) S: Starting model for refinement |
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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 asymmetric unit in this entry is an alpha2beta2 tetramer. the crystallographic asymmetric unit and biological unit are equivalent |
-Components
#1: Protein | Mass: 15096.302 Da / Num. of mol.: 2 / Mutation: V1M, R92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-OXY / #5: 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: 2.54 Å3/Da / Density % sol: 51.55 % |
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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 20% PEG 6000, 10 MM POTASSIUM PHOSPHATE (PH 7.0), 100 MM POTASSIUM CHLORIDE, AND 2.2 MM IHP. THE IHP-STABILIZED CRYSTAL WAS THEN EXPOSED TO 1 ATM OF OXYGEN AT 177K AND DATA WAS COLLECTED AT 169K. |
-Data collection
Diffraction | Mean temperature: 169 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 20, 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: 2.9→43.9 Å / Num. obs: 13441 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2.9→3.13 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2570 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XZ7 Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / SU B: 29.42 / SU ML: 0.559 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.537 / 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: 32.819 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.111 Å / Total num. of bins used: 7 /
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