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Yorodumi- PDB-1cbl: THE 1.9 ANGSTROM STRUCTURE OF DEOXY-BETA4 HEMOGLOBIN: ANALYSIS OF... -
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-Basic information
Entry | Database: PDB / ID: 1cbl | |||||||||
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Title | THE 1.9 ANGSTROM STRUCTURE OF DEOXY-BETA4 HEMOGLOBIN: ANALYSIS OF THE PARTITIONING OF QUATERNARY-ASSOCIATED AND LIGAND-INDUCED CHANGES IN TERTIARY STRUCTURE | |||||||||
Components | HEMOGLOBIN BETA 4 (DEOXY) | |||||||||
Keywords | OXYGEN TRANSPORT | |||||||||
Function / homology | Function and homology information nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / 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 / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | |||||||||
Authors | Borgstahl, G.E.O. / Arnone, A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1994 Title: The 1.9 A structure of deoxy beta 4 hemoglobin. Analysis of the partitioning of quaternary-associated and ligand-induced changes in tertiary structure. Authors: Borgstahl, G.E. / 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 | 1cbl.cif.gz | 129 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cbl.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/1cbl ftp://data.pdbj.org/pub/pdb/validation_reports/cb/1cbl | 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: 15890.198 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P68871 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.2 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Method: batch methodDetails: batch crystallization solution were prepared in a nitrogen-filled globe box | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.83 Å / Num. obs: 46515 / % possible obs: 95.2 % / Num. measured all: 352416 / Rmerge(I) obs: 0.0521 |
-Processing
Software |
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Refinement | Resolution: 1.8→10 Å / σ(F): 2 Details: THE ORTHOGONAL COORDINATE FRAME USED IN THIS ENTRY IS NOT THE DEFAULT ORTHOGONAL COORDINATE FRAME FOR SPACE GROUP P 21.
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.19 / Highest resolution: 1.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 32.8 Å2 |