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- PDB-1jf4: Crystal Structure Of Component IV Glycera Dibranchiata Monomeric ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jf4 | ||||||
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Title | Crystal Structure Of Component IV Glycera Dibranchiata Monomeric Hemoglobin | ||||||
![]() | monomer hemoglobin component IV | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / Glycera / monomer hemoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Park, H.J. / Yang, C. / Treff, N. / Satterlee, J.D. / Kang, C.H. | ||||||
![]() | ![]() Title: Crystal Structures of Unligated and CN-Ligated Glycera dibranchiata Monomer Ferric Hemoglobin Components III and IV Authors: Park, H.J. / Yang, C. / Treff, N. / Satterlee, J.D. / Kang, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41.2 KB | Display | ![]() |
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PDB format | ![]() | 28.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.4 KB | Display | ![]() |
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Full document | ![]() | 465.6 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15049.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.05 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 7, 2000 / Details: mirror |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 12323 / Num. obs: 11627 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 1.4→30 Å / Redundancy: 3.5 % / % possible all: 90 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 10227 / % possible obs: 89 % / Rmerge(I) obs: 0.049 |
Reflection shell | *PLUS Rmerge(I) obs: 36 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 1.4→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 10821 / % reflection Rfree: 5 % / Rfactor obs: 0.189 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.189 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.275 / Rfactor Rwork: 0.234 / Rfactor obs: 0.234 |