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Yorodumi- PDB-4hhb: THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hhb | ||||||||||||||||||
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Title | THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION | ||||||||||||||||||
Components |
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Keywords | OXYGEN TRANSPORT | ||||||||||||||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 / Resolution: 1.74 Å | ||||||||||||||||||
Authors | Fermi, G. / Perutz, M.F. | ||||||||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1984 Title: The crystal structure of human deoxyhaemoglobin at 1.74 A resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R. #1: Journal: Nature / Year: 1982 Title: Stereochemistry of Iron in Deoxyhaemoglobin Authors: Perutz, M.F. / Hasnain, S.S. / Duke, P.J. / Sessler, J.L. / Hahn, J.E. #3: Journal: Annu.Rev.Biochem. / Year: 1979 Title: Regulation of Oxygen Affinity of Hemoglobin. Influence of Structure of the Globin on the Heme Iron Authors: Perutz, M.F. #4: Journal: J.Mol.Biol. / Year: 1976 Title: Three-Dimensional Fourier Synthesis of Human Deoxyhemoglobin at 2.5 Angstroms Resolution, I.X-Ray Analysis Authors: Teneyck, L.F. / Arnone, A. #5: Journal: J.Mol.Biol. / Year: 1975 Title: Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 2.5 Angstroms Resolution, Refinement of the Atomic Model Authors: Fermi, G. #6: Journal: Nature / Year: 1970 Title: Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 3.5 Angstroms Resolution Authors: Muirhead, H. / Greer, J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hhb.cif.gz | 183.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hhb.ent.gz | 104.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hhb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hhb_validation.pdf.gz | 712.4 KB | Display | wwPDB validaton report |
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Full document | 4hhb_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4hhb_validation.xml.gz | 78.5 KB | Display | |
Data in CIF | 4hhb_validation.cif.gz | 95.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/4hhb ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hhb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: PROBABLY PHOSPHATE GROUP. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.952899, 0.301963, -0.028045), Vector: |
-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 / 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 / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.48 % | ||||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: batch method / Details: Perutz, M.F., (1968) J.Crystall Growth, 2, 54. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.74 Å / Lowest resolution: 20 Å / Num. all: 56287 / Num. obs: 54034 / Num. measured all: 292000 / Rmerge(I) obs: 0.067 |
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-Processing
Refinement | Rfactor Rwork: 0.135 / Highest resolution: 1.74 Å Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS. THE Y AXIS IS THE (NON CRYSTALLOGRAPHIC) MOLECULAR DIAD AND THE X AXIS IS THE PSEUDO DIAD WHICH ...Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS. THE Y AXIS IS THE (NON CRYSTALLOGRAPHIC) MOLECULAR DIAD AND THE X AXIS IS THE PSEUDO DIAD WHICH RELATES THE ALPHA-1 AND BETA-1 CHAINS. THE TRANSFORMATION GIVEN IN THE *MTRIX* RECORDS BELOW WILL GENERATE COORDINATES FOR THE *C* AND *D* CHAINS FROM THE *A* AND *B* CHAINS RESPECTIVELY. | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 1.74 Å
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Refinement | *PLUS Rfactor obs: 0.135 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |