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Yorodumi- PDB-2dn3: 1.25A resolution crystal structure of human hemoglobin in the car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dn3 | ||||||
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Title | 1.25A resolution crystal structure of human hemoglobin in the carbonmonoxy form | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / human hemoglobin / high resolution crystal structure / oxygen transport / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Park, S.-Y. / Yokoyama, T. / Shibayama, N. / Shiro, Y. / Tame, J.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: 1.25 a resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. Authors: Park, S.-Y. / Yokoyama, T. / Shibayama, N. / Shiro, Y. / Tame, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dn3.cif.gz | 133.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dn3.ent.gz | 105.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dn3 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dn3 | HTTPS FTP |
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-Related 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 bilogical assembly is a heterotetramer generated from the heterodimer in the aymmetric unit by the operation; Y, X, -Z. |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: red cell / 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) / Tissue: red cell / References: UniProt: P68871 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.26 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 6.7 Details: sodium/potassium phosphate, glycerol, pH 6.7, BATCH, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2000 / Details: Si(iii) |
Radiation | Monochromator: Si(iii) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→25 Å / Num. obs: 76777 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 1.25→1.32 Å / Rmerge(I) obs: 0.533 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→20 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber /
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Refinement step | Cycle: LAST / Resolution: 1.25→20 Å
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Refine LS restraints |
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