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Open data
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Basic information
Entry | Database: PDB / ID: 1s5l | |||||||||
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Title | Architecture of the photosynthetic oxygen evolving center | |||||||||
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![]() | PHOTOSYNTHESIS / photosystem / oxygen-evolving / tetra-manganese / membrane | |||||||||
Function / homology | ![]() photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II ...photosystem II assembly / photosystem II oxygen evolving complex / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthetic electron transport in photosystem II / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ferreira, K.N. / Iverson, T.M. / Maghlaoui, K. / Barber, J. / Iwata, S. | |||||||||
![]() | ![]() Title: Architecture of the Photosynthetic Oxygen-Evolving Center Authors: Ferreira, K.N. / Iverson, T.M. / Maghlaoui, K. / Barber, J. / Iwata, S. | |||||||||
History |
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Remark 999 | SEQUENCE Because the electron density for the two N chains was poor, the authors were unable to ...SEQUENCE Because the electron density for the two N chains was poor, the authors were unable to assign side chains. | |||||||||
Remark 600 | HETEROGEN Ligand PL9 is missing two isoprenoids due to disorder in the electron density. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 987.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 16.4 MB | Display | ![]() |
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Full document | ![]() | 17 MB | Display | |
Data in XML | ![]() | 262 KB | Display | |
Data in CIF | ![]() | 326.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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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2 | ![]()
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Unit cell |
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Details | the biological unit is a dimer, which is present in the asymmetric unit |
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Components
-Protein , 2 types, 4 molecules AaVv
#1: Protein | Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Photosystem II ... , 15 types, 30 molecules BbCcDdHhIiJjKkLlMmOoTtUuXxNnZz
#2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 26851.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #17: Protein/peptide | Mass: 5235.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #18: Protein/peptide | Mass: 3166.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Cytochrome b559 ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Sugars , 1 types, 2 molecules ![](data/chem/img/LMT.gif)
#26: Sugar |
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-Non-polymers , 8 types, 106 molecules ![](data/chem/img/FE.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/OEC.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/OEC.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/HEC.gif)
#20: Chemical | #21: Chemical | ChemComp-BCT / #22: Chemical | #23: Chemical | ChemComp-CLA / #24: Chemical | ChemComp-PHO / #25: Chemical | ChemComp-PL9 / #27: Chemical | ChemComp-BCR / #28: Chemical | ChemComp-HEC / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: pseudo-batch hanging drop / pH: 7.5 Details: 100mM HEPES, 100mM (NH4)2SO4, PEG 4000, C12E8, trimethyl lead acetate, pH 7.5, pseudo-batch hanging drop, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 25, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. all: 117866 / Num. obs: 103604 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 3.5→3.52 Å / % possible all: 80.9 |
Reflection | *PLUS Lowest resolution: 40 Å / % possible obs: 87.3 % / Redundancy: 2.88 % / Num. measured all: 298731 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 80.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2 |
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Processing
Software |
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 3.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection all: 103485 / % reflection Rfree: 1 % / Rfactor Rfree: 0.346 / Rfactor Rwork: 0.303 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3.5 Å / Lowest resolution: 3.56 Å / Rfactor Rfree: 0.384 / Rfactor Rwork: 0.34 |