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Yorodumi- PDB-8el3: Light harvesting phycobiliprotein HaPE555 from the cryptophyte He... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8el3 | ||||||||||||
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Title | Light harvesting phycobiliprotein HaPE555 from the cryptophyte Hemiselmis andersenii CCMP644 in a loose interface filament | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / phycobiliprotein / antenna / light harvesting / cryptophyte / algae / globin / CALM / CaRSP / phycoerythrin / Hemiselmis | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Hemiselmis andersenii (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||||||||
Authors | Rathbone, H.W. / Michie, K.A. / Laos, A.L. / Curmi, P.M.G. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Commun Biol / Year: 2023 Title: Molecular dissection of the soluble photosynthetic antenna from the cryptophyte alga Hemiselmis andersenii. Authors: Rathbone, H.W. / Laos, A.J. / Michie, K.A. / Iranmanesh, H. / Biazik, J. / Goodchild, S.C. / Thordarson, P. / Green, B.R. / Curmi, P.M.G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8el3.cif.gz | 715.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8el3.ent.gz | 591.3 KB | Display | PDB format |
PDBx/mmJSON format | 8el3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/8el3 ftp://data.pdbj.org/pub/pdb/validation_reports/el/8el3 | HTTPS FTP |
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-Related structure data
Related structure data | 7sutC 8el4C 8el5C 8el6C 4lmxS S: Starting model for refinement 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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2 |
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Unit cell |
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-Components
-Phycoerythrin alpha- ... , 2 types, 8 molecules AGJKCEIL
#1: Protein | Mass: 7019.024 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5TBU5 #3: Protein | Mass: 6628.628 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5TBJ3 |
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-Protein , 1 types, 4 molecules BDFH
#2: Protein | Mass: 18406.949 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Hemiselmis andersenii (eukaryote) / References: UniProt: U5T8W0 |
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-Non-polymers , 3 types, 715 molecules
#4: Chemical | ChemComp-PEB / #5: Chemical | ChemComp-AX9 / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 1.88 Å3/Da / Density % sol: 34.47 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: PEG3350 25% (w/v) + NaBr 0.01M, 150nL mother + 150 nL protein stock, Cryoprotectant of 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→48.33 Å / Num. obs: 129756 / % possible obs: 98.2 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.57→1.6 Å / Rmerge(I) obs: 1.399 / Mean I/σ(I) obs: 1 / Num. unique obs: 5326 / CC1/2: 0.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LMX Resolution: 1.57→48.33 Å / SU ML: 0.2128 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8129 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: 23.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→48.33 Å
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Refine LS restraints |
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LS refinement shell |
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