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- PDB-1kd2: Crystal Structure of Human Deoxyhemoglobin in Absence of Any Anions -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kd2 | ||||||
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Title | Crystal Structure of Human Deoxyhemoglobin in Absence of Any Anions | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / HUMAN DEOXY HEMOGLOBIN / HIGH O2 AFFINITY T STATE / CHLORIDE BINDING SITES / ALLOSTERIC ANION BINDING SITES / HYDRATION / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Colombo, M.F. / Seixas, F.A.V. | ||||||
![]() | ![]() Title: The X-Ray Structure of Iso-Ionic Deoxy-Hb Crystal: The High Affinity T-state of Human Hb and the Mechanism of Chloride Regulation of Hb Cooperative Oxygen Binding. Authors: Seixas, F.A.V. / Azevedo Jr, W.F. / Colombo, M.F. #1: ![]() Title: Crystallization and X-ray Diffraction Data Analysis of Human Deoxyhaemoglobin A(0) Fully stripped of Any Anions Authors: Seixas, F.A.V. / Azevedo Jr, W.F. / Colombo, M.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.5 KB | Display | ![]() |
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PDB format | ![]() | 98 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 25.3 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2hhbS 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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Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO ALPHA AND TWO BETA CHAINS. |
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Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 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: 2.48 Å3/Da / Density % sol: 50.4 % |
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Crystal grow | Temperature: 298 K / Method: batch method / pH: 7 Details: DEIONIZED PEG 3350 12.5%, pH 7.0, BATCH METHOD, temperature 298K |
-Data collection
Diffraction | Mean temperature: 299 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 26, 1998 |
Radiation | Monochromator: SILICON CRYSTAL WITH ASYMMETRIC CUT. ASYMMETRIC ANGLE: 7.25 DEGREES, CONDENSATE MODE Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.38 Å / Relative weight: 1 |
Reflection | Resolution: 1.87→69.007 Å / Num. all: 51413 / Num. obs: 51030 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.8 / Rsym value: 0.062 |
Reflection shell | Resolution: 1.87→1.91 Å / Num. unique all: 3240 / Rsym value: 0.348 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2HHB Resolution: 1.87→10 Å / Isotropic thermal model: overall temperature factors / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.062 Å2 | |||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.28 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.87→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.87→1.91 Å
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