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Open data
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Basic information
Entry | Database: PDB / ID: 1y8h | ||||||
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Title | HORSE METHEMOGLOBIN LOW SALT, PH 7.0 | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / AQUO METHEMOGLOBIN / QUARTERNARY ASSOCIATION / ALLOSTERIC TRANSITION / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sankaranarayanan, R. / Biswal, B.K. / Vijayan, M. | ||||||
![]() | ![]() Title: A new relaxed state in horse methemoglobin characterized by crystallographic studies. Authors: Sankaranarayanan, R. / Biswal, B.K. / Vijayan, M. #1: ![]() Title: Structure of Human Methaemoglobin: The Variation of a Theme Authors: Biswal, B.K. / Vijayan, M. #2: ![]() Title: Structures of Human Oxy- and Deoxyhaemoglobin at Different Levels of Humidity: Variability in the T State Authors: Biswal, B.K. / Vijayan, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 118.5 KB | Display | ![]() |
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PDB format | ![]() | 94.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1y8iC ![]() 1y8kC ![]() 2mhbS 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: 15138.280 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: PH 7.0 AQUOMET STRUCTURE / Source: (natural) ![]() ![]() #2: Protein | Mass: 16032.274 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 7 Details: 0.01M Phosphate Buffer, 30%PEG3350, pH 7.0, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 24, 2002 / Details: OSMIC MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→20 Å / Num. obs: 10748 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.188 |
Reflection shell | Resolution: 3.1→3.21 Å / Rmerge(I) obs: 0.511 / Num. unique all: 1028 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HORSE METHEMOGLOBIN, pdb entry 2MHB Resolution: 3.1→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 218152.43 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.0083 Å2 / ksol: 0.23056 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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