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Open data
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Basic information
Entry | Database: PDB / ID: 1buw | ||||||
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Title | CRYSTAL STRUCTURE OF S-NITROSO-NITROSYL HUMAN HEMOGLOBIN A | ||||||
![]() | (PROTEIN (HEMOGLOBIN)) x 2 | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT AND VASODILATION / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() : / nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport ...: / nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / 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 | ![]() | ||||||
![]() | Chan, N.-L. / Rogers, P.H. / Arnone, A. | ||||||
![]() | ![]() Title: Crystal structure of the S-nitroso form of liganded human hemoglobin. Authors: Chan, N.L. / Rogers, P.H. / Arnone, 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 | ![]() | 126.9 KB | Display | ![]() |
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PDB format | ![]() | 100.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 34.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.202601, -0.326635, 0.923181), Vector: |
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Components
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUDATED BLOOD DRAWN FROM HEALTHY NON-SMOKER. / Source: (natural) ![]() #2: Protein | Mass: 15919.196 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: OUDATED BLOOD DRAWN FROM HEALTHY NON-SMOKER. / Source: (natural) ![]() #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-NO / #5: Water | ChemComp-HOH / | Compound details | THIS STRUCTURE PROVIDES THE FIRST DIRECT VISUALIZAT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.06 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5.8 Details: 1% PROTEIN 100 MM SODIUM CACODYLATE, PH 5.8 16% PEG 6000 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Silva, M.M., (1992) J. Biol. Chem., 267, 17248. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Apr 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→20 Å / Num. obs: 55671 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.07 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.77→1.9 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 77 |
Reflection | *PLUS % possible obs: 93 % / Num. measured all: 273695 / Rmerge(I) obs: 0.07 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 1BBB Resolution: 1.9→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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