+Open data
-Basic information
Entry | Database: PDB / ID: 3qjc | ||||||
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Title | Human Hemoglobin A Mutant Beta H63L Carbonmonoxy-Form | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / ligand migration pathways / distal His / globin / oxygen / carbon monoxide / red blood cells | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.001 Å | ||||||
Authors | Birukou, I. / Soman, J. / Olson, J.S. | ||||||
Citation | Journal: Thesis Title: Determination of Pathways for Oxygen Binding to Human HbA Authors: Birukou, I. / Soman, J. / Olson, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qjc.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qjc.ent.gz | 59.9 KB | Display | PDB format |
PDBx/mmJSON format | 3qjc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/3qjc ftp://data.pdbj.org/pub/pdb/validation_reports/qj/3qjc | HTTPS FTP |
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-Related structure data
Related structure data | 3qjbC 3qjdC 3qjeC 2dn3S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69905 | ||||
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#2: Protein | Mass: 15865.210 Da / Num. of mol.: 1 / Mutation: H63L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P68871 | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 293 K / Method: small tubes / pH: 6.7 Details: 2.3 M Na/K phosphate, pH 6.7, SMALL TUBES, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 9, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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→51.371 Å / Num. all: 19713 / Num. obs: 18799 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4 % / Rsym value: 0.098 / Net I/σ(I): 7.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2DN3 Resolution: 2.001→51.371 Å / SU ML: 0.25 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.039 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.001→51.371 Å
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Refine LS restraints |
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LS refinement shell |
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