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Yorodumi- PDB-5oy0: Structure of synechocystis photosystem I trimer at 2.5A resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 5oy0 | |||||||||
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Title | Structure of synechocystis photosystem I trimer at 2.5A resolution | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem I / reaction center / cyanobacteria / electron transfer chain / synechocystis | |||||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...plasma membrane-derived photosystem I / photosystem I reaction center / photosystem I / photosystem I / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.501 Å | |||||||||
Authors | Nelson, N. / Malavath, T. / Caspy, I. | |||||||||
Funding support | Belgium, Israel, 2items
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Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Structure and function of wild-type and subunit-depleted photosystem I in Synechocystis. Authors: Malavath, T. / Caspy, I. / Netzer-El, S.Y. / Klaiman, D. / Nelson, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5oy0.cif.gz | 3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5oy0.ent.gz | 2.7 MB | Display | PDB format |
PDBx/mmJSON format | 5oy0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5oy0_validation.pdf.gz | 86 MB | Display | wwPDB validaton report |
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Full document | 5oy0_full_validation.pdf.gz | 87.7 MB | Display | |
Data in XML | 5oy0_validation.xml.gz | 447.3 KB | Display | |
Data in CIF | 5oy0_validation.cif.gz | 536 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/5oy0 ftp://data.pdbj.org/pub/pdb/validation_reports/oy/5oy0 | 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
-Photosystem I P700 chlorophyll a apoprotein ... , 4 types, 6 molecules AaB2b1
#1: Protein | Mass: 83036.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29254, photosystem I #2: Protein | Mass: 81369.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29255, photosystem I #12: Protein | | Mass: 81167.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29255, photosystem I #16: Protein | | Mass: 82280.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29254, photosystem I |
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-Photosystem I iron-sulfur ... , 2 types, 3 molecules C3c
#3: Protein | Mass: 8706.064 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P32422, photosystem I #13: Protein | | Mass: 8837.261 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P32422, photosystem I |
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-Photosystem I reaction center subunit ... , 14 types, 24 molecules DdE5Ff6IiJj7KLlMm9ek4h80
#4: Protein | Mass: 15663.749 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P19569 #5: Protein | Mass: 7680.478 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P12975 #6: Protein | Mass: 15791.086 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P29256 #7: Protein/peptide | Mass: 4414.148 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55330 #8: Protein/peptide | Mass: 4535.415 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55329 #9: Protein | | Mass: 8237.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74564 #10: Protein | Mass: 16631.795 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P37277 #11: Protein/peptide | Mass: 3382.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P72986 #14: Protein | | Mass: 7552.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P12975 #15: Protein | | Mass: 8037.548 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74564 #17: Protein | | Mass: 15532.552 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P19569 #18: Protein/peptide | | Mass: 4227.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55330 #19: Protein | | Mass: 8124.626 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P74564 #20: Protein | | Mass: 16300.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P37277 |
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-Sugars , 2 types, 6 molecules
#35: Sugar | ChemComp-LMT / #37: Sugar | ChemComp-DGD / | |
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-Non-polymers , 16 types, 1326 molecules
#21: Chemical | ChemComp-CLA / #22: Chemical | ChemComp-PQN / #23: Chemical | ChemComp-SF4 / #24: Chemical | ChemComp-BCR / #25: Chemical | ChemComp-LHG / #26: Chemical | ChemComp-LMG / #27: Chemical | ChemComp-ACT / #28: Chemical | #29: Chemical | #30: Chemical | ChemComp-ECH / #31: Chemical | ChemComp-SQD / #32: Chemical | ChemComp-CA / #33: Chemical | #34: Chemical | ChemComp-ZEX / ( #36: Chemical | ChemComp-EQ3 / ( | #38: Water | ChemComp-HOH / | |
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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: 2.22 Å3/Da / Density % sol: 44.65 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: PEG 3350, magnesium chloride, tricine, glycine, magnesium acetate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 395994 / % possible obs: 99.8 % / Redundancy: 23.3 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 21.8 % / Mean I/σ(I) obs: 0.5 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.501→49.481 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.11 / 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: 2.501→49.481 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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