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- PDB-2peg: Crystal structure of Trematomus bernacchii hemoglobin in a partia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2peg | ||||||
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Title | Crystal structure of Trematomus bernacchii hemoglobin in a partial hemichrome state | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / hemichrome / R/Tintermediate quaternary structure / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vergara, A. / Franzese, M. / Merlino, A. / Vitagliano, L. / Mazzarella, L. | ||||||
![]() | ![]() Title: Structural characterization of ferric hemoglobins from three antarctic fish species of the suborder notothenioidei. Authors: Vergara, A. / Franzese, M. / Merlino, A. / Vitagliano, L. / Verde, C. / di Prisco, G. / Lee, H.C. / Peisach, J. / Mazzarella, L. #1: ![]() Title: The crystal structure of a tetrameric hemoglobin in a partial hemichrome state Authors: Riccio, A. / Vitagliano, L. / di Prisco, G. / Zagari, A. / Mazzarella, L. #2: ![]() Title: The oxidation process of Antarctic fish hemoglobins Authors: Vitagliano, L. / Bonomi, G. / Riccio, A. / di Prisco, G. / Smulevich, G. / Mazzarella, 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 | ![]() | 77.5 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 23.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s5yS 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
#1: Protein | Mass: 15683.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
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#2: Protein | Mass: 16153.368 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: 3.28 Å3/Da / Density % sol: 62.55 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 7.6 Details: PEG MME 5000, TRIS-HCL, pH 7.6, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 1, 2005 / Details: Mirrors |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→30 Å / Num. obs: 74461 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.035 / Χ2: 2.764 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.48→1.53 Å / Rmerge(I) obs: 0.227 / Χ2: 0.676 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1S5Y Resolution: 1.48→30 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.48→30 Å
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Refine LS restraints |
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