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- PDB-6l5y: Carbonmonoxy human hemoglobin A in the R2 quaternary structure at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6l5y | ||||||
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Title | Carbonmonoxy human hemoglobin A in the R2 quaternary structure at 140 K: Light (2 min) | ||||||
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![]() | OXYGEN TRANSPORT / Hemoglobin / Photolysis | ||||||
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 / 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shibayama, N. / Park, S.Y. / Ohki, M. / Sato-Tomita, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Direct observation of ligand migration within human hemoglobin at work. Authors: Shibayama, N. / Sato-Tomita, A. / Ohki, M. / Ichiyanagi, K. / Park, S.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.1 KB | Display | ![]() |
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PDB format | ![]() | 104.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 39 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ka9C ![]() 6kaeC ![]() 6kahC ![]() 6kaiC ![]() 6kaoC ![]() 6kapC ![]() 6kaqC ![]() 6karC ![]() 6kasC ![]() 6katC ![]() 6kauC ![]() 6kavC ![]() 6l5vC ![]() 6l5wC ![]() 6l5xC ![]() 6lcwC ![]() 6lcxC ![]() 1bbbS C: citing same article ( 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: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.42 % |
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Crystal grow | Temperature: 293 K / Method: microbatch / pH: 5.8 Details: 18%w/v PEG 6000, 100 mM sodium cacodylate-hydrochloride buffer, 10%v/v glycerol |
-Data collection
Diffraction | Mean temperature: 140 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 23, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→19.78 Å / Num. obs: 70593 / % possible obs: 98.1 % / Redundancy: 6.5 % / Biso Wilson estimate: 18.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Net I/σ(I): 13.4 / Num. measured all: 459398 / Scaling rejects: 37 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1BBB Resolution: 1.65→19.779 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 97.39 Å2 / Biso mean: 23.6739 Å2 / Biso min: 9.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→19.779 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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