+Open data
-Basic information
Entry | Database: PDB / ID: 5b13 | ||||||
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Title | Crystal structure of phycoerythrin | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Phycobiliprotein | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Palmaria palmata (Dulse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.094 Å | ||||||
Authors | Tanaka, Y. / Gai, Z. / Kishimura, H. | ||||||
Citation | Journal: J FOOD BIOCHEM. / Year: 2016 Title: Structural properties of phycoerythrin from dulse palmaria palmata Authors: Miyabe, Y. / Furuta, T. / Takeda, T. / Kanno, G. / Shimizu, T. / Tanaka, Y. / Gai, Z. / Yasui, H. / Kishimura, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b13.cif.gz | 445.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b13.ent.gz | 373.5 KB | Display | PDB format |
PDBx/mmJSON format | 5b13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b13_validation.pdf.gz | 9.2 MB | Display | wwPDB validaton report |
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Full document | 5b13_full_validation.pdf.gz | 9.3 MB | Display | |
Data in XML | 5b13_validation.xml.gz | 111.6 KB | Display | |
Data in CIF | 5b13_validation.cif.gz | 142.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b13 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b13 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17657.760 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: CYCs are covalently attached to the polypeptide chain. Source: (natural) Palmaria palmata (Dulse) / References: UniProt: F2ZAL8 #2: Protein | Mass: 18425.002 Da / Num. of mol.: 6 / Source method: isolated from a natural source Details: CYC and PUB are covalently attached to the polypeptide chain. Source: (natural) Palmaria palmata (Dulse) / References: UniProt: F2ZAL7 #3: Chemical | ChemComp-CYC / #4: Chemical | ChemComp-PUB / #5: Water | ChemComp-HOH / | 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: 2.73 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium acetate, PEG4000 / PH range: 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 30, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 135827 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rsym value: 0.116 / Net I/σ(I): 11.21 |
Reflection shell | Resolution: 2.09→2.22 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.13 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.094→48.933 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 24.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.094→48.933 Å
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Refine LS restraints |
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LS refinement shell |
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