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- PDB-1j3z: Direct observation of photolysis-induced tertiary structural chan... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j3z | ||||||
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Title | Direct observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Fe-CO)-beta(Ni) hemoglobin (laser unphotolysed) | ||||||
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![]() | OXYGEN STORAGE/TRANSPORT / Tertiary structure changes / Crystal photolysis / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / 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 / 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 / regulation of blood pressure / Chaperone Mediated Autophagy / 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 | ![]() ![]() ![]() | ||||||
![]() | Adachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
![]() | ![]() Title: Direct observation of photolysis-induced tertiary structural changes in hemoglobin Authors: Adachi, S. / Park, S.-Y. / Tame, J.R.H. / Shiro, Y. / Shibayama, 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 | ![]() | 263.7 KB | Display | ![]() |
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PDB format | ![]() | 212.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1j3yC ![]() 1j40C ![]() 1j41C C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 1349 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/HNI.gif)
![](data/chem/img/2FU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/HNI.gif)
![](data/chem/img/2FU.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-CMO / #5: Chemical | ChemComp-HNI / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.7 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 6.6 Details: PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.6 / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 20, 2002 / Details: MONOCHROMATOR |
Radiation | Monochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 144674 / % possible obs: 94.4 % / Observed criterion σ(I): 26 / Redundancy: 3 % / Rmerge(I) obs: 0.035 |
Reflection shell | Resolution: 1.6→1.66 Å / Rmerge(I) obs: 0.096 / % possible all: 83.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 437187 |
Reflection shell | *PLUS % possible obs: 83.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.64 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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