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Yorodumi- PDB-1thb: REFINEMENT OF A PARTIALLY OXYGENATED T STATE HAEMOGLOBIN AT 1.5 A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1thb | |||||||||
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Title | REFINEMENT OF A PARTIALLY OXYGENATED T STATE HAEMOGLOBIN AT 1.5 ANGSTROMS RESOLUTION | |||||||||
Components | (HEMOGLOBIN A ...) x 2 | |||||||||
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: 1.5 Å | |||||||||
Authors | Waller, D.A. / Liddington, R.C. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1990 Title: Refinement of a partially oxygenated T state human haemoglobin at 1.5 A resolution. Authors: Waller, D.A. / Liddington, R.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1thb.cif.gz | 136.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1thb.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 1thb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1thb_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 1thb_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 1thb_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 1thb_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1thb ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thb | HTTPS FTP |
-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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Atom site foot note | 1: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE DENSITY ...1: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE DENSITY AFTER REPEATED EXAMINATION INCLUDING THE USE OF OMIT MAPS. 2: IHP HAS NOT BEEN REFINED OR INCLUDED IN ANY MAP CALCULATION. IHP IS INCLUDED ONLY TO AID IN VISUALIZATION OF WEAK ELECTRON DENSITY AND FOR ILLUSTRATION OF THE BINDING SITE. | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.774, -0.464979, -0.428988), Vector: |
-Components
-HEMOGLOBIN A ... , 2 types, 4 molecules ACBD
#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 |
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-Non-polymers , 4 types, 321 molecules
#3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | ChemComp-IHP / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.21 % | |||||||||||||||
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Crystal grow | *PLUS Method: batch method / PH range low: 7.4 / PH range high: 7.2 | |||||||||||||||
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: 1.5 Å / Num. obs: 73013 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.14 / Biso Wilson estimate: 32.3 Å2 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.5→10 Å / Rfactor obs: 0.196 Details: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE ...Details: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE DENSITY AFTER REPEATED EXAMINATION INCLUDING THE USE OF OMIT MAPS. IHP HAS NOT BEEN REFINED OR INCLUDED IN ANY MAP CALCULATION. IHP IS INCLUDED ONLY TO AID IN VISUALIZATION OF WEAK ELECTRON DENSITY AND FOR ILLUSTRATION OF THE BINDING SITE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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