+Open data
-Basic information
Entry | Database: PDB / ID: 1lfq | ||||||
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Title | OXY HEMOGLOBIN (93% RELATIVE HUMIDITY) | ||||||
Components |
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Keywords | OXYGEN STORAGE/TRANSPORT / HEMOGLOBIN / T State / HUMIDITY / ENVIRONMENT / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / regulation of blood pressure / oxygen binding / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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 / Resolution: 2.6 Å | ||||||
Authors | Biswal, B.K. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state. Authors: Biswal, B.K. / Vijayan, M. #1: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of human oxyhaemoglobin at 2.1 A resolution Authors: Shaanan, B. #2: Journal: J.Mol.Biol. / Year: 1984 Title: The crystal structure of human deoxyhaemoglobin at 1.74 A resolution Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R. #3: Journal: J.Biol.Chem. / Year: 1992 Title: A Third Quaternary Structure of Human Hemoglobin a at 1.7-Angstroms Resolution Authors: Silva, M.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 | 1lfq.cif.gz | 64.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lfq.ent.gz | 48.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lfq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lfq_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1lfq_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1lfq_validation.xml.gz | 14.9 KB | Display | |
Data in CIF | 1lfq_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/1lfq ftp://data.pdbj.org/pub/pdb/validation_reports/lf/1lfq | HTTPS FTP |
-Related structure data
Related structure data | 1jy7C 1lflC 1lftC 1lfvC 1lfyC 1lfzC C: citing same article (ref.) |
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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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905 | ||
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#2: Protein | Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871 | ||
#3: Chemical | #4: 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: 2.32 Å3/Da / Density % sol: 46.87 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.7 / Details: phosphate buffer, pH 6.7, LIQUID DIFFUSION at 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.37 |
-Processing
Software |
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Refinement | Resolution: 2.6→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 77976.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.4878 Å2 / ksol: 0.319158 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
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Xplor file |
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