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Yorodumi- PDB-5nb3: High resolution C-phycoerythrin from marine cyanobacterium Phormi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nb3 | ||||||
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Title | High resolution C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5 | ||||||
Components | (Phycoerythrin ...) x 2 | ||||||
Keywords | PHOTOSYNTHESIS / marine cyanobacterium Phormidium sp.A09DM / C-phycoerythrin / pigment-protein light harvesting complex | ||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
Biological species | Phormidium rubidum A09DM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.38 Å | ||||||
Authors | Sonani, R.R. / Roszak, A.W. / Ortmann de Percin Northumberland, C. / Madamwar, D. / Cogdell, R.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Photosyn. Res. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nb3.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5nb3.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 5nb3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nb3 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nb3 | HTTPS FTP |
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-Related structure data
Related structure data | 5nb4C 5aqdS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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: Two PEB chromophores are covalently linked by residues Cys82 (PEB166) and Cys139 (PEB167) Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A0E3W010 #2: Protein | Mass: 19370.189 Da / Num. of mol.: 12 / Source method: isolated from a natural source Details: Three PEB chromophores are link covalently to Cys80 (PEB186), Cys165 (PEB187), and Cys48/Cys59 (PEB188) Source: (natural) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A0E4G455 |
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-Non-polymers , 7 types, 7913 molecules
#3: Chemical | ChemComp-PEB / #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-MPD / ( #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 2.5 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 G8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→95.42 Å / Num. obs: 932250 / % possible obs: 95.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 8.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.077 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.38→1.42 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 67249 / CC1/2: 0.477 / Rpim(I) all: 0.801 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5aqd Resolution: 1.38→95.42 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.694 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.067 / 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: 15.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→95.42 Å
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Refine LS restraints |
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