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- PDB-1jf3: Crystal Structure Of Component III Glycera Dibranchiata Monomeric... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1jf3 | ||||||
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Title | Crystal Structure Of Component III Glycera Dibranchiata Monomeric Hemoglobin | ||||||
![]() | monomer hemoglobin component III | ||||||
![]() | 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 | ![]() | 41.1 KB | Display | ![]() |
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PDB format | ![]() | 28.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: 14958.023 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: 2.59 Å3/Da / Density % sol: 52.49 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, sodium cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: used microseeding | ||||||||||||||||||||||||||||||
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: Apr 5, 2001 / 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→10 Å / Num. all: 14452 / Num. obs: 11757 / % possible obs: 81.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 1.4→30 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / % possible all: 92 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 9985 / % possible obs: 87 % / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 35 % / Rmerge(I) obs: 0.045 |
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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: 10341 / % reflection Rfree: 5 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.2245 / Rfactor Rwork: 0.188 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.17 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.281 / Rfactor Rwork: 0.241 / Rfactor obs: 0.241 |