+Open data
-Basic information
Entry | Database: PDB / ID: 1s5l | |||||||||
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Title | Architecture of the photosynthetic oxygen evolving center | |||||||||
Components |
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Keywords | PHOTOSYNTHESIS / photosystem / oxygen-evolving / tetra-manganese / membrane | |||||||||
Function / homology | Function and homology information photosystem II oxygen evolving complex / photosystem II assembly / 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 / extrinsic component of membrane ...photosystem II oxygen evolving complex / photosystem II assembly / 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 / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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 | Thermosynechococcus elongatus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.5 Å | |||||||||
Authors | Ferreira, K.N. / Iverson, T.M. / Maghlaoui, K. / Barber, J. / Iwata, S. | |||||||||
Citation | Journal: Science / Year: 2004 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s5l.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1s5l.ent.gz | 987.9 KB | Display | PDB format |
PDBx/mmJSON format | 1s5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1s5l_validation.pdf.gz | 16.4 MB | Display | wwPDB validaton report |
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Full document | 1s5l_full_validation.pdf.gz | 17 MB | Display | |
Data in XML | 1s5l_validation.xml.gz | 262 KB | Display | |
Data in CIF | 1s5l_validation.cif.gz | 326.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/1s5l ftp://data.pdbj.org/pub/pdb/validation_reports/s5/1s5l | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-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 |
-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) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A444 #16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A386 |
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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) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIQ1 #3: Protein | Mass: 51666.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIF8 #4: Protein | Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8CM25 #7: Protein | Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DJZ6 #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P59087 #10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1K9 #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIN8 #12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DHA7 #13: Protein | Mass: 26851.965 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: P0A431 #14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIQ0 #15: Protein | Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1L5 #17: Protein/peptide | Mass: 5235.296 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q9F1R6 #18: Protein/peptide | Mass: 3166.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) #19: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DHJ2 |
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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) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIP0 #6: Protein/peptide | Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / References: UniProt: Q8DIN9 |
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-Sugars , 1 types, 2 molecules
#26: Sugar |
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-Non-polymers , 8 types, 106 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 3.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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 |