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Yorodumi- 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 | ||||||
Components | (Phycoerythrin ...) x 2 | ||||||
Keywords | PHOTOSYNTHESIS / marine cyanobacterium Phormidium sp.A09DM / C-phycoerythrin / PEB chromophore | ||||||
| Function / homology | Function and homology informationphycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | ||||||
| Biological species | Phormidium rubidum A09DM (bacteria) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.14 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: 2018Title: 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. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5nb4.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb5nb4.ent.gz | 1.7 MB | Display | PDB format |
| PDBx/mmJSON format | 5nb4.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5nb4_validation.pdf.gz | 4.5 MB | Display | wwPDB validaton report |
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| Full document | 5nb4_full_validation.pdf.gz | 4.7 MB | Display | |
| Data in XML | 5nb4_validation.xml.gz | 321.3 KB | Display | |
| Data in CIF | 5nb4_validation.cif.gz | 431 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/5nb4 ftp://data.pdbj.org/pub/pdb/validation_reports/nb/5nb4 | 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) 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: 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) Phormidium rubidum A09DM (bacteria) / References: UniProt: A0A0E4G455 |
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-Non-polymers , 7 types, 8286 molecules 












| #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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-Details
| Has protein modification | Y |
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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 C8 with the NPS mix of additives |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
| 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: FOURIER SYNTHESISStarting 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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About Yorodumi



Phormidium rubidum A09DM (bacteria)
X-RAY DIFFRACTION
United States, 1items
Citation












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