+Open data
-Basic information
Entry | Database: PDB / ID: 1jy7 | ||||||
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Title | THE STRUCTURE OF HUMAN METHEMOGLOBIN. THE VARIATION OF A THEME | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / HUMAN METHEMOGLOBIN / OXYGEN TRANSPORT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
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 / Late endosomal microautophagy / oxygen carrier activity / carbon dioxide transport / Heme signaling / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / regulation of blood pressure / platelet aggregation / oxygen binding / 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: 3.2 Å | ||||||
Authors | Biswal, B.K. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state. Authors: Biswal, B.K. / Vijayan, M. #1: Journal: Curr.Sci. / Year: 2001 Title: Structure of human methaemoglobin: The variation of a theme Authors: Biswal, B.K. / Vijayan, M. #2: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of human oxyhaemoglobin at 2.1 A resolution Authors: Shaanan, B. #3: Journal: J.Mol.Biol. / Year: 1984 Title: The Crystal Structure of Human Deoxyhemoglobin at 1.74 Angstroms Resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R. #4: Journal: J.Biol.Chem. / Year: 1992 Title: A third quaternary structure of human hemoglobin A at 1.7-A resolution Authors: Silva, M.M. / 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 | 1jy7.cif.gz | 307.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jy7.ent.gz | 260.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jy7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jy7 ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jy7 | HTTPS FTP |
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-Related structure data
Related structure data | 1lflC 1lfqC 1lftC 1lfvC 1lfyC 1lfzC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / |
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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: 2.53 Å3/Da / Density % sol: 51.4 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 6.7 Details: PEG 4000, Sodium potassium phosphate, pH 6.7, LIQUID DIFFUSION at 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→10 Å / Num. obs: 84268 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.108 |
Reflection shell | Resolution: 3.2→3.3 Å / Rmerge(I) obs: 0.379 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN OXYHEMOGLOBIN Resolution: 3.2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 158735.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.9737 Å2 / ksol: 0.20873 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 85 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.39 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
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Xplor file |
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