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Open data
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Basic information
Entry | Database: PDB / ID: 2wsc | |||||||||
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Title | Improved Model of Plant Photosystem I | |||||||||
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![]() | PHOTOSYNTHESIS / ELECTRON TRANSFER / MEMBRANE PROTEINS / LARGE COMPLEXES | |||||||||
Function / homology | ![]() chloroplast photosystem I / response to low light intensity stimulus / response to high light intensity / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid ...chloroplast photosystem I / response to low light intensity stimulus / response to high light intensity / chloroplast thylakoid / plastoglobule / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / thylakoid / chloroplast envelope / photosystem I / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem I / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / response to cold / chloroplast / phosphoprotein binding / 4 iron, 4 sulfur cluster binding / molecular adaptor activity / oxidoreductase activity / electron transfer activity / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Amunts, A. / Toporik, H. / Borovikov, A. / Nelson, N. | |||||||||
![]() | ![]() Title: Structure Determination and Improved Model of Plant Photosystem I. Authors: Amunts, A. / Toporik, H. / Borovikova, A. / Nelson, N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 851 KB | Display | ![]() |
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PDB format | ![]() | 717.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 57 MB | Display | ![]() |
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Full document | ![]() | 58.6 MB | Display | |
Data in XML | ![]() | 380.9 KB | Display | |
Data in CIF | ![]() | 438.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wseC ![]() 2wsfC ![]() 3lw5C ![]() 1yo9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 5 types, 5 molecules 1234C
#1: Protein | Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 28926.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#3: Protein | Mass: 29852.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Protein | Mass: 27181.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#7: Protein | Mass: 8991.474 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN ... , 2 types, 2 molecules AB
#5: Protein | Mass: 84284.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#6: Protein | Mass: 82490.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-PHOTOSYSTEM I REACTION CENTER SUBUNIT ... , 9 types, 9 molecules DEFGHIJKL
#8: Protein | Mass: 23170.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#9: Protein | Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#10: Protein | Mass: 25445.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 18232.650 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 15341.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#13: Protein/peptide | Mass: 4474.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#14: Protein/peptide | Mass: 5079.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 13742.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#16: Protein | Mass: 22957.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-PHOTOSYSTEM I-N ... , 2 types, 2 molecules NR
#17: Protein | Mass: 18460.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#18: Protein | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Sugars , 2 types, 58 molecules ![](data/chem/img/LMU.gif)
#19: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose #21: Sugar | ChemComp-LMU / |
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-Non-polymers , 6 types, 198 molecules ![](data/chem/img/CLA.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/SF4.gif)
#20: Chemical | ChemComp-CLA / #22: Chemical | ChemComp-BCR / #23: Chemical | #24: Chemical | ChemComp-LMG / | #25: Chemical | #26: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 44 % / Description: NONE |
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Crystal grow | pH: 6 Details: 22.5 MM MES BIS-TRIS PH 6 10MM SUCCINIC ACID 6% PEG6000 0.015% DTM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 88964 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 3.3→3.43 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1YO9 Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.771 / Cor.coef. Fo:Fc free: 0.762 / SU B: 0.001 / SU ML: 0 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Solvent model: NONE | ||||||||||||||||||||
Displacement parameters | Biso mean: 23.117 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→30 Å
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LS refinement shell | Resolution: 3.3→3.385 Å / Total num. of bins used: 20
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