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Yorodumi- PDB-1hdb: ANALYSIS OF THE CRYSTAL STRUCTURE, MOLECULAR MODELING AND INFRARE... -
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-Basic information
Entry | Database: PDB / ID: 1hdb | ||||||
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Title | ANALYSIS OF THE CRYSTAL STRUCTURE, MOLECULAR MODELING AND INFRARED SPECTROSCOPY OF THE DISTAL BETA-HEME POCKET VALINE67(E11)-THREONINE MUTATION OF HEMOGLOBIN | ||||||
Components | (HEMOGLOBIN (DEOXY) BETA-V67T) x 2 | ||||||
Keywords | OXYGEN TRANSPORT / HUMAN HEMOGLOBIN / DEOXY-BETA-V67T | ||||||
Function / homology | Function and homology information : / cellular oxidant detoxification / nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex ...: / cellular oxidant detoxification / 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: 2.2 Å | ||||||
Authors | Pechik, I. / Ji, X. / Fronticelli, C. / Gilliland, G.L. | ||||||
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. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Oxygen Affinity Modulation by the N-Termini of the Beta-Chains in Human and Bovine Hemoglobin Authors: Fronticelli, C. / Pechik, I. / Brinigar, W.S. / Gryczynski, Z. / 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 | 1hdb.cif.gz | 134.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdb.ent.gz | 105.5 KB | Display | PDB format |
PDBx/mmJSON format | 1hdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hdb_validation.pdf.gz | 687.7 KB | Display | wwPDB validaton report |
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Full document | 1hdb_full_validation.pdf.gz | 707 KB | Display | |
Data in XML | 1hdb_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1hdb_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdb ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdb | HTTPS FTP |
-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 / Mutation: CHAIN B, D, V67T Source method: isolated from a genetically manipulated source Details: ALPHA-BETA-ALPHA-BETA TETRAMER / Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-GLOBIN CDNA FUSED TO A / Plasmid: PJK05 (FRONTICELLI ET AL. 1 / Gene (production host): BETA-GLOBIN CDNA FUSED TO A / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P01922, UniProt: P69905*PLUS #2: Protein | Mass: 15892.171 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, V67T Source method: isolated from a genetically manipulated source Details: ALPHA-BETA-ALPHA-BETA TETRAMER / Source: (gene. exp.) Homo sapiens (human) / Gene: BETA-GLOBIN CDNA FUSED TO A / Plasmid: PJK05 (FRONTICELLI ET AL. 1 / Gene (production host): BETA-GLOBIN CDNA FUSED TO A / Production host: Escherichia coli (E. coli) / Strain (production host): AR120 / References: UniProt: P02023, UniProt: P68871*PLUS #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: 2.27 Å3/Da / Density % sol: 45.8 % | ||||||||||||||||||||
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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
Detector | Date: Jul 4, 1994 |
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Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 27163 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 2.75 % |
Reflection | *PLUS Highest resolution: 2.2 Å / Rmerge(I) obs: 0.07 |
-Processing
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Refinement | Resolution: 2.2→6 Å / σ(F): 2 /
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Displacement parameters | Biso mean: 21.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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