[English] 日本語
![](img/lk-miru.gif)
- PDB-6yq8: Crystal structure of native Phycocyanin from T. elongatus in spac... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6yq8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of native Phycocyanin from T. elongatus in spacegroup P63 at 1.8 Angstroms | ||||||
![]() | (C-phycocyanin ...) x 2 | ||||||
![]() | PHOTOSYNTHESIS / Native C-Phycocyanin / antenna protein / heterodimer / ligand-bound / Phycobilisome / Chromophore / ELECTRON TRANSPORT | ||||||
Function / homology | ![]() phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Feiler, C.G. / Falke, S. / Sarrou, I. | ||||||
![]() | ![]() Title: C-phycocyanin as a highly attractive model system in protein crystallography: unique crystallization properties and packing-diversity screening. Authors: Sarrou, I. / Feiler, C.G. / Falke, S. / Peard, N. / Yefanov, O. / Chapman, H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 254.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 175.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6ypqSC ![]() 6yqgC ![]() 6yyjC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
-C-phycocyanin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 17456.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: BP-1 / Gene: cpcA, tlr1958 Production host: ![]() ![]() References: UniProt: P50032 |
---|---|
#2: Protein | Mass: 18216.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Residue 72: N4-methylasparagine; parent Asn Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P50033 |
-Non-polymers , 5 types, 237 molecules ![](data/chem/img/CYC.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PGE / #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1% Nucleosides Mix, 0.1M Buffer System3, 50% Precipitant Mix 3, Morpheus Screen |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→44.32 Å / Num. obs: 48140 / % possible obs: 99.96 % / Redundancy: 11.13 % / Biso Wilson estimate: 41.34 Å2 / Rrim(I) all: 0.06 / Net I/σ(I): 22.21 |
Reflection shell | Resolution: 1.82→1.94 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 4751 / Rrim(I) all: 0.267 / % possible all: 99.81 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6YPQ Resolution: 1.82→44.32 Å / SU ML: 0.2443 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7206
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→44.32 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|