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Yorodumi- PDB-4kt0: Crystal structure of a virus like photosystem I from the cyanobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kt0 | |||||||||
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Title | Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803 | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / photosynthetic reaction center / membrane complex / plastocyanin / cytochrome C6 / Ferredoxin | |||||||||
Function / homology | Function and homology information plasma membrane-derived photosystem I / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding ...plasma membrane-derived photosystem I / thylakoid membrane / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Mazor, Y. / Nataf, D. / Toporik, H. / Nelson, N. | |||||||||
Citation | Journal: Elife / Year: 2014 Title: Crystal structures of virus-like photosystem I complexes from the mesophilic cyanobacterium Synechocystis PCC 6803. Authors: Mazor, Y. / Nataf, D. / Toporik, H. / Nelson, N. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kt0.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4kt0.ent.gz | 972.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kt0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4kt0 ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4kt0 | HTTPS FTP |
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-Related structure data
Related structure data | 4l6vC 1jb0S S: Starting model for refinement C: citing same article (ref.) |
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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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Details | AUTHOR STATED THAT THERE IS NO QUATERNARY STRUCTURE FOR THIS ENTRY. PISA FAILED TO GENERATE ASSEMBLY. THEREFORE THE ASU IS INDICATED AS ASSEMBLY TEMPORARILY. |
-Components
-Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 83036.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: 10HIS tag was added to the C terminus of PsaL. The mutated chain is lost during purification. Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: Synechocystis sp. PCC 6803 / Gene: BEST7613_2234, MYO_18690, psaA References: UniProt: L8AHT3, UniProt: P29254*PLUS, photosystem I |
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#2: Protein | Mass: 81369.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaB, BEST7613_2235, MYO_18700 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8AIC0, UniProt: P29255*PLUS, photosystem I |
-Photosystem I subunit ... , 2 types, 2 molecules DF
#4: Protein | Mass: 15663.749 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaD, BEST7613_1459, MYO_11100 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8AFM8, UniProt: P19569*PLUS, photosystem I |
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#6: Protein | Mass: 18267.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaF, BEST7613_2928 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8AII8, UniProt: P29256*PLUS, photosystem I |
-Photosystem I reaction center subunit ... , 4 types, 4 molecules EJKM
#5: Protein | Mass: 8154.086 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaE, BEST7613_5968, MYO_118260 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8ASH8, UniProt: P12975*PLUS, photosystem I |
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#7: Protein/peptide | Mass: 4535.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaJ, BEST7613_2927, MYO_115450 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8AGL9, UniProt: Q55329*PLUS, photosystem I |
#8: Protein | Mass: 13732.274 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaK, BEST7613_4536, MYO_129960 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8APJ0, UniProt: P74564*PLUS, photosystem I |
#9: Protein/peptide | Mass: 3382.063 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psbM, psaM, BEST7613_1787, MYO_14340 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8ADF9, UniProt: P72986*PLUS, photosystem I |
-Protein / Sugars , 2 types, 3 molecules C
#16: Sugar | #3: Protein | | Mass: 8837.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: psaC, BEST7613_5694, MYO_120930 / Production host: Synechocystis sp. PCC 6803 (bacteria) References: UniProt: L8AST2, UniProt: P32422*PLUS, photosystem I |
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-Non-polymers , 9 types, 149 molecules
#10: Chemical | #11: Chemical | #12: Chemical | ChemComp-LHG / #13: Chemical | #14: Chemical | ChemComp-BCR / #15: Chemical | ChemComp-CLA / #17: Chemical | ChemComp-LMG / | #18: Chemical | ChemComp-CL / | #19: 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: 3.94 Å3/Da / Density % sol: 68.75 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 4.5% PEG3350, 30mM Tricine-NaOH pH8, 55mM NaCl, 50mM Glycine, 0.005% Nonyl- beta -D-Maltoside., pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 16, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. all: 92450 / Num. obs: 91895 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 61.4 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.382 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JB0 with truncated side chains and chlorophyll tails Resolution: 2.8→29.977 Å / SU ML: 0.4 / Isotropic thermal model: single parameter per residue. / σ(F): 1.35 / Phase error: 28.46 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→29.977 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -9.005 Å / Origin y: -7.8261 Å / Origin z: 21.7491 Å
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Refinement TLS group | Selection details: chain A or chain B or chain C or chain D or chain E or chain F or chain J or chain K or chain M |