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Yorodumi- PDB-7qu4: Recombinant Human Fetal Hemoglobin mutant - alpha subunit mutatio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qu4 | |||||||||
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Title | Recombinant Human Fetal Hemoglobin mutant - alpha subunit mutations K11E,K56E,N78D,K90E | |||||||||
Components |
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Keywords | OXYGEN TRANSPORT / Globin / Hemoglobin | |||||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process ...nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / 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 / oxygen binding / peroxidase activity / Factors involved in megakaryocyte development and platelet production / blood microparticle / iron ion binding / heme binding / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | |||||||||
Authors | Kettisen, K. / Nyblom, M. / Bulow, L. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Front Mol Biosci / Year: 2023 Title: Structural and oxidative investigation of a recombinant high-yielding fetal hemoglobin mutant. Authors: Kettisen, K. / Nyblom, M. / Smeds, E. / Fago, A. / Bulow, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qu4.cif.gz | 168.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qu4.ent.gz | 107.3 KB | Display | PDB format |
PDBx/mmJSON format | 7qu4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qu4_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7qu4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7qu4_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | 7qu4_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7qu4 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qu4 | HTTPS FTP |
-Related structure data
Related structure data | 1bz1S 1fdhS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 16148.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69892 #2: Protein | Mass: 15282.337 Da / Num. of mol.: 2 / Mutation: K11E,K56E,N78D,K90E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905 #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.44 Å3/Da / Density % sol: 49.63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Sodium fluoride, 0.1 M Bis-Tris propane pH 6.5, 20 % (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.657→54.463 Å / Num. obs: 72637 / % possible obs: 98.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.657→1.685 Å / Num. unique obs: 3568 / CC1/2: 0.774 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BZ1,1FDH Resolution: 1.66→52.946 Å / SU ML: 0.1848 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6836 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→52.946 Å
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Refine LS restraints |
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LS refinement shell |
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