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Yorodumi- PDB-2x20: Structure of Peridinin-Chlorophyll-Protein reconstituted with Chl-b -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x20 | ||||||
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Title | Structure of Peridinin-Chlorophyll-Protein reconstituted with Chl-b | ||||||
Components | PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC | ||||||
Keywords | PHOTOSYNTHESIS / LIGHT-HARVESTING POLYPEPTIDE / LIGHT HARVESTING PROTEIN / ALPHA HELICAL / CHROMOPHORE / CHLOROPLAST / CAROTENOIDS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | AMPHIDINIUM CARTERAE (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Schulte, T. / Hiller, R.G. / Hofmann, E. | ||||||
Citation | Journal: FEBS Lett. / Year: 2010 Title: X-Ray Structures of the Peridinin-Chlorophyll-Protein Reconstituted with Different Chlorophylls. Authors: Schulte, T. / Hiller, R.G. / Hofmann, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x20.cif.gz | 64 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x20.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 2x20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/2x20 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/2x20 | HTTPS FTP |
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-Related structure data
Related structure data | 2x1zC 2x21C 3iisS C: citing same article (ref.) 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
-Protein / Sugars , 2 types, 2 molecules M
#1: Protein | Mass: 15954.204 Da / Num. of mol.: 1 / Fragment: RESIDUES 57-207 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMPHIDINIUM CARTERAE (eukaryote) / Strain: CS-21 / Plasmid: PND707 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P80484 |
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#4: Sugar | ChemComp-DGD / |
-Non-polymers , 8 types, 213 molecules
#2: Chemical | ChemComp-CHL / | ||||||||||||
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#3: Chemical | ChemComp-PID / #5: Chemical | ChemComp-CD / #6: Chemical | #7: Chemical | ChemComp-K / | #8: Chemical | ChemComp-NA / | #9: Chemical | ChemComp-PEG / | #10: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 44.69 % / Description: NONE |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M CDCL2, 0,1M SODIUM ACETATE PH 4.6, 20-24% PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 9, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→43.15 Å / Num. obs: 15738 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.9 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3IIS Resolution: 1.95→43.15 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.003 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.131 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.99 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→43.15 Å
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Refine LS restraints |
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