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Yorodumi- PDB-6y3d: X-ray structure of thermophilic C-phycocyanin from Galdiera phlegrea -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y3d | ||||||
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Title | X-ray structure of thermophilic C-phycocyanin from Galdiera phlegrea | ||||||
Components | (C-phycocyanin ...) x 2 | ||||||
Keywords | FLUORESCENT PROTEIN / red algae / C-phycocyanin / pigment / fluorescent / Phycobilisomes | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cyanidium caldarium (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ferraro, G. / Lucignano, R. / Marseglia, A. / Merlino, A. | ||||||
Citation | Journal: Biochim Biophys Acta Bioenerg / Year: 2020 Title: X-ray structure of C-phycocyanin from Galdieria phlegrea: Determinants of thermostability and comparison with a C-phycocyanin in the entire phycobilisome. Authors: Ferraro, G. / Imbimbo, P. / Marseglia, A. / Lucignano, R. / Monti, D.M. / Merlino, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6y3d.cif.gz | 427.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y3d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6y3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/6y3d ftp://data.pdbj.org/pub/pdb/validation_reports/y3/6y3d | HTTPS FTP |
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-Related structure data
Related structure data | 3brpS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-C-phycocyanin ... , 2 types, 12 molecules AAACCCEEEGGGIIIKKKBBBDDDFFFHHHJJJLLL
#1: Protein | Mass: 17260.398 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19910 #2: Protein | Mass: 18203.604 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19909 |
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-Non-polymers , 4 types, 1236 molecules
#3: Chemical | ChemComp-CYC / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.10 M Hepes, 0.20 M magnesium chloride and 9.0 % (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.96 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 2, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→94.744 Å / Num. obs: 217082 / % possible obs: 92.5 % / Redundancy: 4.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.119 / Rrim(I) all: 0.255 / Net I/σ(I): 2.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.8 / Num. unique obs: 30323 / CC1/2: 0.061 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3brp Resolution: 1.8→94.744 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.529 / SU ML: 0.193 / Cross valid method: FREE R-VALUE / ESU R: 0.143 / ESU R Free: 0.142 Details: Hydrogens have been added in their 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.779 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→94.744 Å
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Refine LS restraints |
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LS refinement shell |
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