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- PDB-1kr7: Crystal structure of the nerve tissue mini-hemoglobin from the ne... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1kr7 | ||||||
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Title | Crystal structure of the nerve tissue mini-hemoglobin from the nemertean worm Cerebratulus lacteus | ||||||
![]() | Neural globin | ||||||
![]() | OXYGEN STORAGE/TRANSPORT / nerve tissue / mini-hemoglobin / protein cavities / Oxygen transport / OXYGEN STORAGE-TRANSPORT COMPLEX | ||||||
Function / homology | ![]() oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pesce, A. / Nardini, M. / Dewilde, S. / Geuens, E. / Yamauchi, k. / Ascenzi, P. / Riggs, A.F. / Moens, L. / Bolognesi, M. | ||||||
![]() | ![]() Title: The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the alpha-helical globin fold Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Geuens, E. / Yamauchi, k. / Ascenzi, P. / Riggs, A.F. / Moens, L. / Bolognesi, M. #1: ![]() Title: Crystallization and preliminary X-ray analysis of neural hemoglobin from the nemertean worm Cerebratulus lacteus Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Ascenzi, P. / Riggs, A.F. / Yamauchi, K. / Geuens, E. / Moens, L. / Bolognesi, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.8 KB | Display | ![]() |
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PDB format | ![]() | 44.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 834.8 KB | Display | ![]() |
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Full document | ![]() | 835.7 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11546.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET3a / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 110 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-HEM / |
#5: Chemical | ChemComp-OXY / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.5 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ammonium sulfate, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
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: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001 / Details: mirrors | ||||||||||||
Radiation | Monochromator: Si 311 channel and Si 111 channel cut / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→35 Å / Num. all: 17906 / Num. obs: 17906 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 14.3 | ||||||||||||
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1168 / Rsym value: 0.239 / % possible all: 95.7 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 35 Å / Num. measured all: 67606 / Rmerge(I) obs: 0.054 | ||||||||||||
Reflection shell | *PLUS % possible obs: 95.7 % / Rmerge(I) obs: 0.239 |
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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 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→35.14 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 35 Å / Rfactor all: 0.1563 / Rfactor obs: 0.153 / Rfactor Rfree: 0.18702 / Rfactor Rwork: 0.15298 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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