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- PDB-7e97: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 58% oxygen ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7.0E+97 | |||||||||
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Title | Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 58% oxygen saturation | |||||||||
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![]() | OXYGEN TRANSPORT / allostery / structural change / microspectrometry / crystal processing. | |||||||||
Function / homology | ![]() hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Numoto, N. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state. Authors: Numoto, N. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.3 KB | Display | ![]() |
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PDB format | ![]() | 94.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 22.9 KB | Display | |
Data in CIF | ![]() | 29.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7e96C ![]() 7e98C ![]() 7e99C ![]() 2zfoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Components
-Extracellular giant hemoglobin major globin subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 15188.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 15327.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 15621.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 14693.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 3 types, 25 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-HEM / #6: Chemical | ChemComp-OXY / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 11-12 % (w/v) polyethylene glycol (PEG) 10,000, 10 mM CaCl2, 200 mM Tris-HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 18081 / % possible obs: 99.8 % / Redundancy: 9.7 % / Biso Wilson estimate: 59.17 Å2 / CC1/2: 0.998 / Rsym value: 0.208 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.7→2.87 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2846 / CC1/2: 0.583 / Rsym value: 1.37 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZFO Resolution: 2.7→47.4 Å / SU ML: 0.3498 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0503 / Stereochemistry target values: GeoStd + Monomer Library
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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: 61.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→47.4 Å
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Refine LS restraints |
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LS refinement shell |
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