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Yorodumi- PDB-1hbb: HIGH-RESOLUTION X-RAY STUDY OF DEOXYHEMOGLOBIN ROTHSCHILD 37BETA ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hbb | |||||||||
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Title | HIGH-RESOLUTION X-RAY STUDY OF DEOXYHEMOGLOBIN ROTHSCHILD 37BETA TRP-> ARG: A MUTATION THAT CREATES AN INTERSUBUNIT CHLORIDE-BINDING SITE | |||||||||
Components |
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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 / regulation of blood pressure / 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 / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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: 1.9 Å | |||||||||
Authors | Kavanaugh, J.S. / Arnone, A. | |||||||||
Citation | Journal: Biochemistry / Year: 1992 Title: High-resolution X-ray study of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site. Authors: Kavanaugh, J.S. / Rogers, P.H. / Case, D.A. / Arnone, A. #1: Journal: J.Mol.Biol. / Year: 1984 Title: The Crystal Structure of Human Deoxyheamoglobin at 1.74 Angstroms Resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. #2: Journal: J.Biol.Chem. / Year: 1987 Title: Specifically Carboxymethylated Hemoglobin as an Analogue of Carbamino Hemoglobin: Solution and X-Ray Studies of Carboxymethylated Hemoglobin and X-Ray Studies of Carbamino Hemoglobin Authors: Fantl, W.J. / Didonato, A. / Manning, J.M. / 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 | 1hbb.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hbb.ent.gz | 101 KB | Display | PDB format |
PDBx/mmJSON format | 1hbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hbb_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 1hbb_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1hbb_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 1hbb_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/1hbb ftp://data.pdbj.org/pub/pdb/validation_reports/hb/1hbb | HTTPS FTP |
-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: (0.775363, 0.457539, -0.4323), 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) / 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) / 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: 2.56 Å3/Da / Density % sol: 51.93 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: batch method / pH: 7 | ||||||||||||||||||||||||||||||
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: 1.91 Å / Num. obs: 47999 / % possible obs: 95 % / Num. measured all: 18175 / Rmerge(I) obs: 0.044 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.185 / Highest resolution: 1.9 Å Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM THAT IS STANDARD FOR TETRAMERIC HEMOGLOBINS. THE Y AXIS IS A NONCRYSTALLOGRAPHIC MOLECULAR DIAD, AND THE X AXIS IS A PSEUDO ...Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM THAT IS STANDARD FOR TETRAMERIC HEMOGLOBINS. THE Y AXIS IS A NONCRYSTALLOGRAPHIC MOLECULAR DIAD, AND THE X AXIS IS A PSEUDO DIAD THAT RELATES THE ALPHA-1 SUBUNIT TO THE BETA-1 SUBUNIT (AND ALPHA-2 TO BETA-2). COORDINATES ARE GIVEN FOR THE FULL TETRAMER. SUBUNIT LABELS A, B, C, AND D REFER TO SUBUNITS A1, B1, A2, AND B2, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL GENERATE APPROXIMATE COORDINATES FOR THE ALPHA2-BETA2 DIMER WHEN APPLIED TO THE ALPHA1-BETA1 DIMER. THE CELL DIMENSIONS PRESENTED ON THE CRYST1 RECORD BELOW ARE THOSE THAT WERE USED IN THE REFINEMENT. PLEASE NOTE THAT SOME DIFFERENCES EXIST IN THE FIRST DECIMAL PLACE BETWEEN THESE VALUES AND THE CELL DIMENSIONS PUBLISHED IN THE 1992 BIOCHEMISTRY PAPER. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / Num. reflection obs: 44919 / σ(I): 2 / Rfactor obs: 0.185 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |