+Open data
-Basic information
Entry | Database: PDB / ID: 1yzi | ||||||
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Title | A novel quaternary structure of human carbonmonoxy hemoglobin | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / hemoglobin / allosteric / quaternary / high affinity / relaxed / tense / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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: 2.07 Å | ||||||
Authors | Safo, M.K. / Abraham, D.J. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: The enigma of the liganded hemoglobin end state: a novel quaternary structure of human carbonmonoxy hemoglobin. Authors: Safo, M.K. / Abraham, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yzi.cif.gz | 74.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yzi.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/1yzi ftp://data.pdbj.org/pub/pdb/validation_reports/yz/1yzi | HTTPS FTP |
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-Related structure data
Related structure data | 1mkoC 1hhoS 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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Components on special symmetry positions |
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Details | The biological assembly is a tetramer generated by the two-fold axis: 1-Y,1-X,1/4-Z |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: red blood cells / References: UniProt: P69905 |
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#2: Protein | Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: red blood cells / References: UniProt: P68871 |
-Non-polymers , 4 types, 143 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #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: 2.56 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 298 K / Method: small tubes / pH: 7.1 Details: sodium/potassium phosphate, toluene, pH 7.1, SMALL TUBES, temperature 298K |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 26, 2002 / Details: mirrors |
Radiation | Monochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→58 Å / Num. all: 20310 / Num. obs: 21330 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.07→2.2 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2 / Num. unique all: 2522 / % possible all: 76.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1HHO Resolution: 2.07→58 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 146006.75 / 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: 66.0968 Å2 / ksol: 0.364174 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.07→58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.07→2.2 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
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Xplor file |
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