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Yorodumi- PDB-2dn2: 1.25A resolution crystal structure of human hemoglobin in the deo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dn2 | |||||||||
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Title | 1.25A resolution crystal structure of human hemoglobin in the deoxy 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 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 / 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 | 2dn2.cif.gz | 243.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dn2.ent.gz | 197.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/2dn2 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/2dn2 | HTTPS FTP |
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-Related structure data
Related structure data | 2dn1C 2dn3C 1a3nS 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 biological assembly is a heterotetramaer of the asymmetric unit. |
-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: red cell / 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: red cell / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: 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: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 6.5 Details: Ammonium sulfate, Ammonium phosphate, pH 6.5, Batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 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: Jul 25, 2005 / 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: 145478 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.25→1.32 Å / Rmerge(I) obs: 0.465 / % possible all: 93.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1A3N Resolution: 1.25→20 Å / Isotropic thermal model: Anisotropic / 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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