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- PDB-6rp5: Crystal structure of monocarboxylated hemoglobin from the sub-Ant... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rp5 | ||||||
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Title | Crystal structure of monocarboxylated hemoglobin from the sub-Antarctic fish Eleginops maclovinus | ||||||
![]() | (Hemoglobin subunit ...![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Balasco, N. / Vitagliano, L. / Merlino, A. / Verde, C. / Mazzarella, L. / Vergara, A. | ||||||
![]() | ![]() Title: The unique structural features of carbonmonoxy hemoglobin from the sub-Antarctic fish Eleginops maclovinus. Authors: Balasco, N. / Vitagliano, L. / Merlino, A. / Verde, C. / Mazzarella, L. / Vergara, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.1 KB | Display | ![]() |
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PDB format | ![]() | 61.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4esaS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Hemoglobin subunit ... , 2 types, 2 molecules AB
#1: Protein | ![]() Mass: 15686.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | ![]() Mass: 15852.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 5 types, 395 molecules ![](data/chem/img/CMO.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DTN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DTN.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ![]() #4: Chemical | ![]() #5: Chemical | ChemComp-SO4 / ![]() #6: Chemical | ChemComp-DTN / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.25 Å3/Da / Density % sol: 62.11 % |
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Crystal grow![]() | Temperature: 277 K / Method: microdialysis Details: CO atmosphere , 20 mg/ml protein, 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: May 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.49→79.42 Å / Num. obs: 66710 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.057 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.49→1.53 Å / Rmerge(I) obs: 0.44 / Num. unique obs: 5202 / Rpim(I) all: 0.295 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4ESA Resolution: 1.49→79.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.679 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.07 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.598 Å2
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Refinement step | Cycle: 1 / Resolution: 1.49→79.42 Å
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Refine LS restraints |
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