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Open data
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Basic information
Entry | Database: PDB / ID: 1a9w | ||||||
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Title | HUMAN EMBRYONIC GOWER II CARBONMONOXY HEMOGLOBIN | ||||||
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![]() | OXYGEN TRANSPORT | ||||||
Function / homology | ![]() nitric oxide transport / cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process ...nitric oxide transport / cellular oxidant detoxification / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / response to organic cyclic compound / Cytoprotection by HMOX1 / oxygen binding / blood coagulation / Factors involved in megakaryocyte development and platelet production / blood microparticle / iron ion binding / heme binding / protein-containing complex binding / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sutherland-Smith, A.J. / Baker, H.M. / Hofmann, O.M. / Brittain, T. / Baker, E.N. | ||||||
![]() | ![]() Title: Crystal structure of a human embryonic haemoglobin: the carbonmonoxy form of gower II (alpha2 epsilon2) haemoglobin at 2.9 A resolution. Authors: Sutherland-Smith, A.J. / Baker, H.M. / Hofmann, O.M. / Brittain, T. / Baker, E.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 | ![]() | 112.6 KB | Display | ![]() |
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PDB format | ![]() | 88.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1bbbS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HUMAN GOWER II EMBRYONIC HEMOGLOBIN / Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 16094.614 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HUMAN GOWER II EMBRYONIC HEMOGLOBIN / Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: microseeding, macroseeding used to increase crystal size pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 21% MME-PEG 5000, 0.2M TAPS/ KOH, PH 8.5, 2MM DITHIONITE. THEN MICROSEEDING AND MACROSEEDING USED TO INCREASE CRYSTAL SIZE, microseeding and macroseeding used ...Details: PROTEIN WAS CRYSTALLIZED FROM 21% MME-PEG 5000, 0.2M TAPS/ KOH, PH 8.5, 2MM DITHIONITE. THEN MICROSEEDING AND MACROSEEDING USED TO INCREASE CRYSTAL SIZE, microseeding and macroseeding used to increase crystal size | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1994 / Details: 0.3 MM COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. obs: 14645 / % possible obs: 95.9 % / Observed criterion σ(I): 1.9 / Redundancy: 5.9 % / Biso Wilson estimate: 61.7 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.9→2.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.37 / % possible all: 76.3 |
Reflection | *PLUS Num. obs: 14597 / Num. measured all: 118919 |
Reflection shell | *PLUS % possible obs: 72.6 % / Rmerge(I) obs: 0.417 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BBB Resolution: 2.9→40 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 Isotropic thermal model: ONE B FOR MAIN CHAIN ATOM B FOR SIDE CHAIN ATOMS Cross valid method: THROUGHOUT / σ(F): 0 / Details: TNT-5E ALSO USED
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Displacement parameters | Biso mean: 50.3 Å2
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Refine analyze | Luzzati sigma a obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→40 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 2.9→3.03 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 / Rfactor Rfree: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.97 Å / Rfactor Rfree: 0.366 / Rfactor obs: 0.301 |