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- PDB-5nb4: Atomic resolution structure of C-phycoerythrin from marine cyanob... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nb4 | ||||||
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Title | Atomic resolution structure of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5 | ||||||
![]() | (Phycoerythrin ...) x 2 | ||||||
![]() | PHOTOSYNTHESIS / marine cyanobacterium Phormidium sp.A09DM / C-phycoerythrin / PEB chromophore | ||||||
Function / homology | ![]() phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sonani, R.R. / Roszak, A.W. / Ortmann de Percin Northumberland, C. / Madamwar, D. / Cogdell, R.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An improved crystal structure of C-phycoerythrin from the marine cyanobacterium Phormidium sp. A09DM. Authors: Sonani, R.R. / Roszak, A.W. / Ortmann de Percin Northumberland, C. / Madamwar, D. / Cogdell, R.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | 1.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 24 MB | Display | ![]() |
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Full document | ![]() | 24.2 MB | Display | |
Data in XML | ![]() | 119 KB | Display | |
Data in CIF | ![]() | 196.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nb3C ![]() 5aqdS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Phycoerythrin ... , 2 types, 24 molecules ABCDEFGHIJKLMNOPQRSTUVWX
#1: Protein | Mass: 17660.830 Da / Num. of mol.: 12 / Source method: isolated from a natural source Details: There are two PEB chromophore molecules in the alpha-subunit covalently bound to residues Cys82 (PEB166) and Cys139 (PEB167). Source: (natural) ![]() #2: Protein | Mass: 19370.189 Da / Num. of mol.: 12 / Source method: isolated from a natural source Details: There are three PEB chromophore molecules in the beta-subunit which are bound covalently to residues Cys80 (PEB186), Cys165 (PEB187) and Cys48/Cys59 (PEB188). Source: (natural) ![]() |
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-Non-polymers , 7 types, 8286 molecules ![](data/chem/img/PEB.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/PI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/PI.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/MRD.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEB / #4: Chemical | ChemComp-NO3 / #5: Chemical | ChemComp-PI / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-MPD / ( #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus screen condition C8 with the NPS mix of additives |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→94.62 Å / Num. obs: 1575226 / % possible obs: 93.8 % / Redundancy: 2.6 % / Biso Wilson estimate: 9.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.042 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.14→1.16 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 74960 / CC1/2: 0.601 / Rpim(I) all: 0.545 / % possible all: 90 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5aqd Resolution: 1.14→94.62 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.53 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.14→94.62 Å
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Refine LS restraints |
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