+Open data
-Basic information
Entry | Database: PDB / ID: 6hbw | ||||||
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Title | Crystal structure of deoxy-human hemoglobin beta6 glu->trp | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / HEMOGLOBIN / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin 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 / 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 / blood microparticle / ficolin-1-rich granule lumen / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Harrington, D.J. / Adachi, K. / Royer Jr., W.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1998 Title: Crystal structure of deoxy-human hemoglobin beta6 Glu --> Trp. Implications for the structure and formation of the sickle cell fiber. Authors: Harrington, D.J. / Adachi, K. / Royer Jr., W.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hbw.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hbw.ent.gz | 104 KB | Display | PDB format |
PDBx/mmJSON format | 6hbw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/6hbw ftp://data.pdbj.org/pub/pdb/validation_reports/hb/6hbw | HTTPS FTP |
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-Related structure data
Related structure data | 2hhbS S: Starting model for refinement |
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Similar 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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: RED BLOOD CELLS / Cellular location: CYTOPLASM / Plasmid: PGS389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P69905 #2: Protein | Mass: 15947.296 Da / Num. of mol.: 2 / Mutation: E6W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: BLOOD / Cell: RED BLOOD CELLS / Cellular location: CYTOPLASM / Plasmid: PGS389 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): GSY112 / References: UniProt: P68871 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.27 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: PROTEIN WAS RESUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 160 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN ...Details: PROTEIN WAS RESUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 160 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN SOLUTION, 5 UL CITRATE BUFFER (PH 4.0), AND 4UL OF 33% PEG 8K. | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→100 Å / Num. obs: 35597 / % possible obs: 89.2 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 13.8 Å2 / Rsym value: 0.076 |
Reflection shell | Resolution: 2→2.09 Å / Rsym value: 0.371 / % possible all: 70.3 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 112861 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 70.3 % / Rmerge(I) obs: 0.371 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2HHB Resolution: 2→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3260377.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 14 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 35002 / Num. reflection Rfree: 2112 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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