[English] 日本語
![](img/lk-miru.gif)
- PDB-4kt0: Crystal structure of a virus like photosystem I from the cyanobac... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4kt0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of a virus like photosystem I from the cyanobacterium Synechocystis PCC 6803 | |||||||||
![]() |
| |||||||||
![]() | ELECTRON TRANSPORT / photosynthetic reaction center / membrane complex / plastocyanin / cytochrome C6 / Ferredoxin | |||||||||
Function / homology | ![]() plasma membrane-derived photosystem I / thylakoid membrane / 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 ...plasma membrane-derived photosystem I / thylakoid membrane / 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 / membrane => GO:0016020 / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mazor, Y. / Nataf, D. / Toporik, H. / Nelson, N. | |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 972.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 27.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 27.6 MB | Display | |
Data in XML | ![]() | 144.9 KB | Display | |
Data in CIF | ![]() | 176.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4l6vC ![]() 1jb0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() References: UniProt: L8AHT3, UniProt: P29254*PLUS, photosystem I |
---|---|
#2: Protein | Mass: 81369.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() References: UniProt: L8AFM8, UniProt: P19569*PLUS, photosystem I |
---|---|
#6: Protein | Mass: 18267.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() References: UniProt: L8ASH8, UniProt: P12975*PLUS, photosystem I |
---|---|
#7: Protein/peptide | Mass: 4535.415 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() 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.) ![]() ![]() ![]() ![]() References: UniProt: L8ADF9, UniProt: P72986*PLUS, photosystem I |
-Protein / Sugars , 2 types, 3 molecules C![](data/chem/img/LMU.gif)
![](data/chem/img/LMU.gif)
#16: Sugar | #3: Protein | | Mass: 8837.261 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: L8AST2, UniProt: P32422*PLUS, photosystem I |
---|
-Non-polymers , 9 types, 149 molecules ![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/CL0.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/CL0.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.75 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -9.005 Å / Origin y: -7.8261 Å / Origin z: 21.7491 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |