+Open data
-Basic information
Entry | Database: PDB / ID: 2dxm | ||||||
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Title | Neutron Structure Analysis of Deoxy Human Hemoglobin | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / alpha2-beta2 / 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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Morimoto, Y. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography. Authors: Chatake, T. / Shibayama, N. / Park, S.Y. / Kurihara, K. / Tamada, T. / Tanaka, I. / Niimura, N. / Kuroki, R. / Morimoto, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dxm.cif.gz | 230.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dxm.ent.gz | 193.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/2dxm ftp://data.pdbj.org/pub/pdb/validation_reports/dx/2dxm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-DOD / | |
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-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Method: microdialysis / Details: D2O, MICRODIALYSIS |
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-B / Wavelength: 2.9 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron |
Radiation wavelength | Wavelength: 2.9 Å / Relative weight: 1 |
Reflection | Resolution: 2→62.5 Å / Num. all: 56073 / Num. obs: 21841 / % possible obs: 70.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.099 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Deoxy Human HB X-ray model(unpublished) Resolution: 2.1→8 Å / σ(F): 1 / σ(I): 1
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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