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Yorodumi- PDB-1yvt: The high salt (phosphate) crystal structure of CO Hemoglobin E (G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yvt | ||||||
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Title | The high salt (phosphate) crystal structure of CO Hemoglobin E (Glu26Lys) at physiological pH (pH 7.35) | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / Hemoglobin E oxygen transport beta thalassemia physiological | ||||||
Function / homology | Function and homology information cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / 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 / 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 / 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 / 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: 1.8 Å | ||||||
Authors | Malashkevich, V.N. / Balazs, T.C. / Almo, S.C. / Hirsch, R.E. | ||||||
Citation | Journal: To be Published Title: The high salt (phosphate) crystal structure of CO Hemoglobin E (Glu26Lys) at physiological pH (pH 7.35) Authors: Malashkevich, V.N. / Balazs, T.C. / Almo, S.C. / Hirsch, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yvt.cif.gz | 78.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yvt.ent.gz | 57.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/1yvt ftp://data.pdbj.org/pub/pdb/validation_reports/yv/1yvt | HTTPS FTP |
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-Related structure data
Related structure data | 1rvwS 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 | Biological assembly is a tetramer. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1 / Production host: Mus musculus (house mouse) / References: UniProt: P69905 |
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#2: Protein | Mass: 15890.265 Da / Num. of mol.: 1 / Mutation: E26K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Mus musculus (house mouse) / References: UniProt: P68871 |
-Non-polymers , 4 types, 291 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: 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: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 289 K / pH: 7.35 Details: 1.65M potassium phosphate, 0.1M HEPES, ph 7.35, Batch Method, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 20, 2004 / Details: Osmic |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 26842 / Num. obs: 26762 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2597 / Rsym value: 0.457 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RVW Resolution: 1.8→22.41 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1772081.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.3815 Å2 / ksol: 0.384459 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→22.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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