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Open data
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Basic information
Entry | Database: PDB / ID: 1cg5 | ||||||
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Title | DEOXY FORM HEMOGLOBIN FROM DASYATIS AKAJEI | ||||||
![]() | (PROTEIN (HEMOGLOBIN)) x 2 | ||||||
![]() | OXYGEN TRANSPORT | ||||||
Function / homology | ![]() hemoglobin complex / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chong, K.T. / Morimoto, H. | ||||||
![]() | ![]() Title: Structures of the deoxy and CO forms of haemoglobin from Dasyatis akajei, a cartilaginous fish. Authors: Chong, K.T. / Miyazaki, G. / Morimoto, H. / Oda, Y. / 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 | ![]() | 74 KB | Display | ![]() |
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PDB format | ![]() | 54.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 14.5 KB | Display | |
Data in CIF | ![]() | 19.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cg8C ![]() 2hhbS 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
#1: Protein | Mass: 15861.097 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
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#2: Protein | Mass: 16315.638 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % | |||||||||||||||
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Crystal grow | pH: 6.5 / Details: pH 6.5 | |||||||||||||||
Crystal grow | *PLUS Method: batch method | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→100 Å / Num. obs: 42219 / % possible obs: 92.7 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 1 / % possible all: 78.1 |
Reflection | *PLUS Num. measured all: 209235 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / % possible obs: 78.1 % / Num. unique obs: 3544 / Num. measured obs: 16933 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HHB Resolution: 1.6→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 16.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.191 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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