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Open data
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Basic information
Entry | Database: PDB / ID: 1o1k | ||||||
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Title | Deoxy hemoglobin (A,C:V1M; B,D:V1M,V67W) | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / HEME / OXYGEN DELIVERY VEHICLE / BLOOD SUBSTITUTE / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() 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 / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Brucker, E.A. | ||||||
![]() | #1: ![]() Title: Genetically Crosslinked Hemoglobin: A Structural Study Authors: Brucker, E.A. #2: ![]() Title: Rate of Reaction with Nitric Oxide Determines the Hypertensive Effect of Cell-Free Hemoglobin Authors: Doherty, D.H. / Doyle, M.P. / Curry, S.R. / Vali, R.J. / Fattor, T.J. / Olson, J.S. / Lemon, D.D. #3: ![]() Title: A Human Recombinant Hemoglobin Designed for Use as a Blood Substitute Authors: Looker, D. / Abbot-Brown, D. / Cozart, P. / Durfee, S. / Hoffman, S. / Mathews, A.J. / Miller-Roehrich, J. / Shoemaker, S. / Trimble, S. / Fermi, G. / Komiyama, N.H. / Nagai, K. / Stetler, G.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.8 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 34.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1c7cS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15182.419 Da / Num. of mol.: 2 / Mutation: V1M Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 16009.343 Da / Num. of mol.: 2 / Mutation: V1M, V67W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | pH: 6.5 / Details: pH 6.50 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 15, 1998 / 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→30 Å / Num. obs: 26599 / % possible obs: 71 % / Redundancy: 2.17 % / Biso Wilson estimate: 5.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.68 / % possible all: 75.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1C7C Resolution: 2→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 18.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINED / Rms dev position: 0.028 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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