+Open data
-Basic information
Entry | Database: PDB / ID: 8ow6 | ||||||
---|---|---|---|---|---|---|---|
Title | PERIDININ-CHLOROPHYLL-PROTEIN OF HETEROCAPSA PYGMAEA, 100K | ||||||
Components | (Peridinin-chl a ...) x 2 | ||||||
Keywords | PHOTOSYNTHESIS / Light Harvesting / Carotenoid / Chlorophyll / Lipid / Dinoflagellates | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Heterocapsa pygmaea (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Hofmann, E. / Schulte, T. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: To Be Published 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8ow6.cif.gz | 505.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8ow6.ent.gz | 369.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ow6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/8ow6 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8ow6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 8ov5C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
|
-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) Heterocapsa pygmaea (eukaryote) / Strain: UCSB-5M29 / References: UniProt: Q9FEY4 #2: Protein | Mass: 15670.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Heterocapsa pygmaea (eukaryote) / Strain: UCSB-5M29 |
---|
-Non-polymers , 7 types, 847 molecules
#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 / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.14 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9788 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→43.5 Å / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 27.0822 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|