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Yorodumi- PDB-3kzi: Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kzi | |||||||||
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Title | Crystal Structure of Monomeric Form of Cyanobacterial Photosystem II | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / ELECTRON TRANSPORT PHOTOSYSTEM / PS II / PS2 / MEMBRANE COMPLEX / TRANSMEMBRANE ALPHA-HELIX / IRON / METAL-BINDING / PHOTOSYNTHESIS / PHOTOSYSTEM II / THYLAKOID / HEME / REACTION CENTER / MANGANESE | |||||||||
Function / homology | Function and homology information photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / 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 / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | |||||||||
Authors | Gabdulkhakov, A. / Guskov, A. / Broser, M. / Kern, J. / Zouni, A. / Saenger, W. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Crystal Structure of Monomeric Photosystem II from Thermosynechococcus elongatus at 3.6-A Resolution Authors: Broser, M. / Gabdulkhakov, A. / Kern, J. / Guskov, A. / Muh, F. / Saenger, W. / Zouni, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kzi.cif.gz | 636.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kzi.ent.gz | 521.6 KB | Display | PDB format |
PDBx/mmJSON format | 3kzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzi ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzi | HTTPS FTP |
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-Related structure data
Related structure data | 3bz1 S: Starting model for refinement |
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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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-Components
-Protein , 2 types, 2 molecules AV
#1: Protein | Mass: 38265.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A444 |
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#16: Protein | Mass: 15148.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A386 |
-Photosystem II ... , 15 types, 15 molecules BCDHIJKLMOTUyXZ
#2: Protein | Mass: 56656.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1 |
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#3: Protein | Mass: 50287.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIF8 |
#4: Protein | Mass: 39388.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8CM25 |
#7: Protein | Mass: 7227.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJ43 |
#8: Protein/peptide | Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJZ6 |
#9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P59087 |
#10: Protein/peptide | Mass: 4101.911 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1K9 |
#11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN8 |
#12: Protein/peptide | Mass: 3981.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHA7 |
#13: Protein | Mass: 26851.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: P0A431 |
#14: Protein/peptide | Mass: 3878.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ0 |
#15: Protein | Mass: 11655.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1L5 |
#17: Protein/peptide | Mass: 5039.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1 |
#18: Protein/peptide | Mass: 4191.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6 |
#19: Protein | Mass: 6766.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2 |
-Cytochrome b559 subunit ... , 2 types, 2 molecules EF
#5: Protein | Mass: 9449.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIP0 |
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#6: Protein/peptide | Mass: 4936.704 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIN9 |
-Sugars , 2 types, 15 molecules
#28: Sugar | ChemComp-DGD / #29: Sugar | ChemComp-LMT / |
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-Non-polymers , 13 types, 72 molecules
#20: Chemical | ChemComp-FE2 / | ||||||||||||||||||||||
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#21: Chemical | ChemComp-CLA / #22: Chemical | #23: Chemical | ChemComp-MES / | #24: Chemical | ChemComp-OEC / | #25: Chemical | ChemComp-BCR / #26: Chemical | #27: Chemical | ChemComp-LMG / #30: Chemical | ChemComp-SQD / #31: Chemical | ChemComp-BCT / | #32: Chemical | ChemComp-PL9 / | #33: Chemical | #34: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.78 Å3/Da / Density % sol: 67.44 % |
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Crystal grow | Temperature: 291 K / Method: batch / pH: 7 Details: PEG 400, PIPES, MES, CaCl2, pH 7, batch, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2008 |
Radiation | Monochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→30 Å / Num. all: 53178 / Num. obs: 47417 / % possible obs: 89.2 % / Observed criterion σ(I): 1 / Redundancy: 4.11 % / Rmerge(I) obs: 0.112 / Rsym value: 0.075 / Net I/σ(I): 11.35 |
Reflection shell | Resolution: 3.6→3.7 Å / Redundancy: 4.24 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.34 / Num. unique all: 2829 / Rsym value: 0.638 / % possible all: 68.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BZ1 3bz1 Resolution: 3.6→29.87 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 11330360.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 102.888 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 162.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.6→29.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.83 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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