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Yorodumi- PDB-1dxt: HIGH-RESOLUTION X-RAY STUDY OF DEOXY RECOMBINANT HUMAN HEMOGLOBIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dxt | |||||||||
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Title | HIGH-RESOLUTION X-RAY STUDY OF DEOXY RECOMBINANT HUMAN HEMOGLOBINS SYNTHESIZED FROM BETA-GLOBINS HAVING MUTATED AMINO TERMINI | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT | |||||||||
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 | X-RAY DIFFRACTION / Resolution: 1.7 Å | |||||||||
Authors | Kavanaugh, J.S. / Arnone, A. | |||||||||
Citation | Journal: Biochemistry / Year: 1992 Title: High-resolution X-ray study of deoxy recombinant human hemoglobins synthesized from beta-globins having mutated amino termini. Authors: Kavanaugh, J.S. / Rogers, P.H. / Arnone, A. #1: Journal: Biochemistry / Year: 1992 Title: Functional Properties of Human Hemoglobins Synthesized from Recombinant Mutant Beta-Globins Authors: Doyle, M.L. / Lew, G. / Deyoung, A. / Kwiatkowski, L. / Wierzbra, A. / Noble, R.W. / Ackers, G.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dxt.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dxt.ent.gz | 101.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dxt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dxt ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dxt | 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.949218, 0.312922, -0.029915), Vector: Details | IN THE ORTHOGONAL COORDINATE SPACE, THE HB TETRAMER HAS BEEN ORIENTED WITH ITS MOLECULAR DYAD ALONG THE Y-AXIS. THE A1B1 DIMER CAN BE TRANSFORMED APPROXIMATELY ONTO TO A2B2 DIMER BY THE *MTRIX* RECORDS BELOW. | |
-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) / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #2: Protein | Mass: 16021.396 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68871 #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: 2.25 Å3/Da / Density % sol: 45.3 % | |||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: microdialysis | |||||||||||||||
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: 1.8 Å / Num. obs: 46131 / % possible obs: 90 % / Num. measured all: 148393 / Rmerge(I) obs: 0.034 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.7→6 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 1.7→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 46508 / σ(F): 2 / Rfactor obs: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |