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Open data
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Basic information
Entry | Database: PDB / ID: 8ow6 | ||||||
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Title | PERIDININ-CHLOROPHYLL-PROTEIN OF HETEROCAPSA PYGMAEA, 100K | ||||||
![]() | (Peridinin-chl a ...) x 2 | ||||||
![]() | PHOTOSYNTHESIS / Light Harvesting / Carotenoid / Chlorophyll / Lipid / Dinoflagellates | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hofmann, E. / Schulte, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Spectroscopic Characterization of the Peridinin-Chlorophyll a-Protein (PCP) Complex from Heterocapsa pygmaea (HPPCP) Authors: Schulte, T. / Magdaong, N.C.M. / Di Valentin, M. / Agostini, A. / Tait, C.E. / Niedzwiedzki, D.M. / Carbonera, D. / Hofmann, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 505.9 KB | Display | ![]() |
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PDB format | ![]() | 369.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.5 MB | Display | |
Data in XML | ![]() | 39.7 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ov5C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 |
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Unit cell |
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Components
-Peridinin-chl a ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15707.830 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 15670.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 7 types, 847 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/PID.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PID.gif)
![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CLA / #4: Chemical | ChemComp-PID / #5: Chemical | ChemComp-W4O / [( Mass: 933.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H80O15 / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | #7: Chemical | ChemComp-PO4 / | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.14 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.82 M NaH2PO4 1.24 M K2HPO4 100 mM Na-acetate at pH 5.5 100 mM LiSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→43.5 Å / Num. obs: 227100 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.119 / Net I/σ(I): 8.11 |
Reflection shell | Resolution: 1.2→1.23 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.31 / Num. unique obs: 16634 / CC1/2: 0.386 / Rrim(I) all: 0.942 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.04 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→43.5 Å
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Refine LS restraints |
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LS refinement shell |
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