[English] 日本語
![](img/lk-miru.gif)
- PDB-8el5: Light harvesting phycobiliprotein HaPE555 from the cryptophyte He... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8el5 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Light harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in an alternating tight to loose interface filament | ||||||||||||
![]() |
| ||||||||||||
![]() | PHOTOSYNTHESIS / phycobiliprotein / antenna / light harvesting / cryptophyte / algae / globin / CALM / CaRSP / phycoerythrin / Hemiselmis | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Rathbone, H.W. / Michie, K.A. / Laos, A.L. / Curmi, P.M.G. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii. Authors: Rathbone, H.W. / Laos, A.J. / Michie, K.A. / Iranmanesh, H. / Biazik, J. / Goodchild, S.C. / Thordarson, P. / Green, B.R. / Curmi, P.M.G. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 714.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 592.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7sutC ![]() 8el3C ![]() 8el4C ![]() 8el6C ![]() 4lmxS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-
Components
-Phycoerythrin alpha- ... , 2 types, 8 molecules AGJKCEIL
#1: Protein | Mass: 7019.024 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 6628.628 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Protein , 1 types, 4 molecules BDFH
#2: Protein | Mass: 18406.949 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
---|
-Non-polymers , 4 types, 365 molecules ![](data/chem/img/PEB.gif)
![](data/chem/img/AX9.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AX9.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-PEB / #5: Chemical | ChemComp-AX9 / #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.78 Å3/Da / Density % sol: 30.96 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 25% PEG3350 (w/v) + 2% (w/v) Benzamidine HCl, 150 nL mother + 150 nl protein solution, Cryoprotectant of 20% Gylcerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→61.7 Å / Num. obs: 104433 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.67→1.7 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5125 / CC1/2: 0.406 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4LMX Resolution: 1.67→61.66 Å / SU ML: 0.2914 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6129 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.67→61.66 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|