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Yorodumi- PDB-1r1x: Crystal structure of oxy-human hemoglobin Bassett at 2.15 angstrom -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r1x | ||||||
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Title | Crystal structure of oxy-human hemoglobin Bassett at 2.15 angstrom | ||||||
Components |
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Keywords | OXYGEN TRANSPORT / hemoglobin / carbon monoxide / mutant / Rochester / oxygen affinity | ||||||
Function / homology | Function and homology information nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin 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 / 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 / oxygen binding / regulation of blood pressure / 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 / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Abdulmalik, O. / Safo, M.K. / Lerner, N.B. / Ochotorena, J. / Dhaikin, Y. / Abraham, D.J. / Asakura, T. | ||||||
Citation | Journal: Am.J.Hematol. / Year: 2004 Title: Characterization of hemoglobin bassett (alpha94Asp-->Ala), a variant with very low oxygen affinity Authors: Abdulmalik, O. / Safo, M.K. / Lerner, N.B. / Ochotorena, J. / Daikhin, Y. / Lakka, V. / Santacroce, R. / Abraham, D.J. / Asakura, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r1x.cif.gz | 75.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1x.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r1x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r1x_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1r1x_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1r1x_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 1r1x_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1x ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1x | HTTPS FTP |
-Related structure data
Related structure data | 1r1yC 1ljwS 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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Details | The biological assembly is tetramer generated from the dimer in the asymmetric unit by the symmetry operations: 1-Y, 1-X, 1/2-Z. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 15106.343 Da / Num. of mol.: 1 / Mutation: D94A / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / 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) / Tissue: blood / References: UniProt: P68871 |
-Non-polymers , 4 types, 198 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.2 Å3/Da / Density % sol: 44.14 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.7 Details: potassium/Sodium phosphate, toluene, hemoglobin, pH 6.7, LIQUID DIFFUSION, temperature 298K |
Crystal grow | *PLUS Method: unknown / Details: Perutz, M.F., (1968) J. Crystal Growth, 2, 54. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 19, 2002 / Details: MSC Confocal Mirrors |
Radiation | Monochromator: MSC Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→95.74 Å / Num. all: 15985 / Num. obs: 14996 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 2.1 / Num. unique all: 739 / % possible all: 72.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB Entry 1LJW Resolution: 2.15→51.41 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 94016.48 / Data cutoff high rms absF: 94016.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.9604 Å2 / ksol: 0.3427 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→51.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.281 / Rfactor Rwork: 0.218 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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