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- PDB-1g9v: HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN COMPLEXED W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g9v | ||||||
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Title | HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXY HEMOGLOBIN COMPLEXED WITH A POTENT ALLOSTERIC EFFECTOR | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / Hemoglobin Tetramer / T state / Allosteric / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / cellular oxidant detoxification / hemoglobin binding / hemoglobin alpha 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 / regulation of blood pressure / Late endosomal microautophagy / 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 / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / Factors involved in megakaryocyte development and platelet production / tertiary granule lumen / 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 | ![]() ![]() | ||||||
![]() | Safo, M.K. / Moure, C.M. / Burnett, J.C. / Joshi, G.S. / Abraham, D.J. | ||||||
![]() | ![]() Title: High-resolution crystal structure of deoxy hemoglobin complexed with a potent allosteric effector. Authors: Safo, M.K. / Moure, C.M. / Burnett, J.C. / Joshi, G.S. / Abraham, D.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.8 KB | Display | ![]() |
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PDB format | ![]() | 102.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 36.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hhb 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 | Biological assembly is a tetramer in the asymmetric unit |
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Components
-Protein , 2 types, 4 molecules ACBD
#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) ![]() |
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-Non-polymers , 4 types, 268 molecules ![](data/chem/img/HEM.gif)
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![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/RQ3.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6.5 Details: Ammonium sulfate, ammonium phosphate, ferrous citrate, pH 6.5, LIQUID DIFFUSION, temperature 298K |
Crystal grow | *PLUS Method: batch method |
Components of the solutions | *PLUS Conc.: 3.6 M / Common name: sulfate/phosphate |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 6, 1997 / Details: mirrors |
Radiation | Monochromator: MSC mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→55 Å / Num. all: 44139 / Num. obs: 44139 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.26 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.85→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3912 / % possible all: 85.1 |
Reflection | *PLUS Lowest resolution: 55 Å / Num. measured all: 165826 |
Reflection shell | *PLUS % possible obs: 85.1 % / Num. unique obs: 3912 / Num. measured obs: 14162 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1HHB ![]() 1hhb Resolution: 1.85→55 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh and Huber Details: Anomalous data used for refinement. Bulk solvent correction used during refinement.
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Displacement parameters | Biso mean: 22.2 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å
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Software | *PLUS Name: ![]() | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 55 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.177 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.2 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.348 / Rfactor Rwork: 0.328 / Rfactor obs: 0.328 |