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Yorodumi- PDB-8xf1: Crystal structure of the dissociated C-phycocyanin beta-chain fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xf1 | |||||||||
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Title | Crystal structure of the dissociated C-phycocyanin beta-chain from Thermoleptolyngbya sp. O-77 | |||||||||
Components | C-phycocyanin beta chain | |||||||||
Keywords | PHOTOSYNTHESIS / dissociated subunit / C-phycocyanin | |||||||||
Function / homology | PHYCOCYANOBILIN Function and homology information | |||||||||
Biological species | Leptolyngbya sp. O-77 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å | |||||||||
Authors | Nguyen, H.K. / Teramoto, T. / Kakuta, Y. / Yoon, K.S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Biosci.Bioeng. / Year: 2024 Title: Disassembly and reassembly of the non-conventional thermophilic C-phycocyanin. Authors: Nguyen, H.K. / Minato, T. / Teramoto, T. / Ogo, S. / Kakuta, Y. / Yoon, K.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xf1.cif.gz | 49.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xf1.ent.gz | 34.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xf1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xf1_validation.pdf.gz | 1016.3 KB | Display | wwPDB validaton report |
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Full document | 8xf1_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8xf1_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 8xf1_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/8xf1 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/8xf1 | HTTPS FTP |
-Related structure data
Related structure data | 8xf0C 8xf2C 8xf3C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18097.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Leptolyngbya sp. O-77 (bacteria) | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.2 M Mg(CH3COO)2 4H2O |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 26569 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.94→2.05 Å / Num. unique obs: 4294 / CC1/2: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→48.87 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→48.87 Å
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Refine LS restraints |
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LS refinement shell |
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