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Yorodumi- PDB-4v82: Crystal structure of cyanobacterial Photosystem II in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v82 | ||||||||||||
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Title | Crystal structure of cyanobacterial Photosystem II in complex with terbutryn | ||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / TRANSMEMBRANE ALPHA-HELIX / PS II / PS2 / ELECTRON TRANSPORT PHOTOSYSTEM / HERBICIDE RESISTANCE / PHOTOSYSTEM II / REACTION CENTER / IRON / METAL-BINDING / HEME / MANGANESE / MEMBRANE COMPLEX / THYLAKOID | ||||||||||||
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 / photosystem II ...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 / 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 | Thermosynechococcus elongatus (bacteria) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||||||||
Authors | Gabdulkhakov, A. / Broser, M. / Guskov, A. / Kern, J. / Glockner, C. / Muh, F. / Saenger, W. / Zouni, A. | ||||||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn Authors: Broser, M. / Glockner, C. / Gabdulkhakov, A. / Guskov, A. / Buchta, J. / Kern, J. / Muh, F. / Dau, H. / 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 | 4v82.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v82.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v82 ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v82 | 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, 4 molecules AABAAVBV
#1: Protein | Mass: 38265.625 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / 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) / Strain: BP-1 / References: UniProt: P0A386 |
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-Photosystem II ... , 16 types, 32 molecules ABBBACBCADBDAHBHAIBIAJBJAKBKALBLAMBMAOBOATBTAUBUAyByAXBXAYBYAZBZ
#2: Protein | Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DIQ1 #3: Protein | Mass: 50287.500 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / 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) / Strain: BP-1 / 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) / Strain: BP-1 / 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) / Strain: BP-1 / 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) / Strain: BP-1 / 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) / Strain: BP-1 / 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) / Strain: BP-1 / References: UniProt: Q8DHA7 #13: Protein | Mass: 26923.045 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DJI1 #18: Protein/peptide | Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q9F1R6 #19: Protein/peptide | Mass: 2400.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) THERMOSYNECHOCOCCUS ELONGATUS (bacteria) / Strain: BP-1 #20: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / References: UniProt: Q8DHJ2 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules AEBEAFBF
#5: Protein | Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus elongatus (bacteria) / Strain: BP-1 / 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) / Strain: BP-1 / References: UniProt: Q8DIN9 |
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-Sugars , 2 types, 30 molecules
#28: Sugar | ChemComp-DGD / #32: Sugar | ChemComp-LMT / |
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-Non-polymers , 15 types, 164 molecules
#21: Chemical | #22: Chemical | #23: Chemical | #24: Chemical | ChemComp-CLA / #25: Chemical | #26: Chemical | #27: Chemical | ChemComp-BCR / #29: Chemical | ChemComp-LHG / #30: Chemical | ChemComp-SQD / #31: Chemical | ChemComp-LMG / #33: Chemical | ChemComp-DMS / #34: Chemical | ChemComp-PHO / #35: Chemical | #36: Chemical | ChemComp-HEM / #37: Chemical | ChemComp-CA / |
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-Details
Sequence details | CHAIN Y:THE DEPOSITORS KNOW THE SEQUENCE. BUT THEY DON'T KNOW IF THE FIRST RESIDUE OF THE CHAIN IS ...CHAIN Y:THE DEPOSITORS |
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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: 3.63 Å3/Da / Density % sol: 66.14 % |
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Crystal grow | Temperature: 298 K / Method: batch / pH: 7 Details: Pipes, CaCl2, DMSO, PEG 2000, pH 7.0, batch, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2009 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 137557 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.93 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.158 / Rsym value: 0.129 / Net I/σ(I): 7.76 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 5.07 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.34 / Num. unique all: 12582 / Rsym value: 0.588 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BZ1 3bz1 Resolution: 3.2→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 7881267.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.0364 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 120.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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