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Yorodumi- PDB-2hhd: OXYGEN AFFINITY MODULATION BY THE N-TERMINI OF THE BETA-CHAINS IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hhd | ||||||
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Title | OXYGEN AFFINITY MODULATION BY THE N-TERMINI OF THE BETA-CHAINS IN HUMAN AND BOVINE HEMOGLOBIN | ||||||
Components |
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Keywords | OXYGEN TRANSPORT | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Gilliland, G.L. / Pechik, I. / Fronticelli, C. / Ji, X. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Crystallographic, molecular modeling, and biophysical characterization of the valine beta 67 (E11)-->threonine variant of hemoglobin. Authors: Pechik, I. / Ji, X. / Fidelis, K. / Karavitis, M. / Moult, J. / Brinigar, W.S. / Fronticelli, C. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hhd.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hhd.ent.gz | 105.6 KB | Display | PDB format |
PDBx/mmJSON format | 2hhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/2hhd ftp://data.pdbj.org/pub/pdb/validation_reports/hh/2hhd | 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
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Organ: BLOOD / References: UniProt: P01922, UniProt: P69905*PLUS #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Organ: BLOOD / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Water | ChemComp-HOH / | Source details | PURIFIED FROM OUTDATED BLOOD OBTAINED FROM THE BLOOD BANK OF THE UNIVERSITY | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.92 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: batch method / Details: Perutz, M.F., (1968) J.Crystal Growth, 2, 54. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | Num. obs: 27357 / % possible obs: 93 % |
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Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Rmerge(I) obs: 0.08 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.2→6 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 16.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.137 / Rfactor Rwork: 0.137 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |