+Open data
-Basic information
Entry | Database: PDB / ID: 3a0h | |||||||||
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Title | Crystal structure of I-substituted Photosystem II complex | |||||||||
Components |
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Keywords | ELECTRON TRANSPORT / MULTI-MEMBRANE PROTEIN COMPLEX / Herbicide resistance / Iron / Membrane / Metal-binding / Photosynthesis / Photosystem II / Thylakoid / Transmembrane / Transport / Heme / Reaction center | |||||||||
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 / protein stabilization / electron transfer activity / iron ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermosynechococcus vulcanus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | |||||||||
Authors | Kawakami, K. / Umena, Y. / Kamiya, N. / Shen, J.-R. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography Authors: Kawakami, K. / Umena, Y. / Kamiya, N. / Shen, J.-R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a0h.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3a0h.ent.gz | 1001.7 KB | Display | PDB format |
PDBx/mmJSON format | 3a0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a0h_validation.pdf.gz | 19.9 MB | Display | wwPDB validaton report |
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Full document | 3a0h_full_validation.pdf.gz | 21 MB | Display | |
Data in XML | 3a0h_validation.xml.gz | 361.4 KB | Display | |
Data in CIF | 3a0h_validation.cif.gz | 422.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/3a0h ftp://data.pdbj.org/pub/pdb/validation_reports/a0/3a0h | HTTPS FTP |
-Related structure data
Related structure data | 3a0bC 2axtS C: citing same article (ref.) 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 AaVv
#1: Protein | Mass: 38295.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P51765 #16: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P0A387 |
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-Photosystem II ... , 16 types, 32 molecules BbCcDdHhIiJjKkLlMmOoTtUuXxYyNnZz
#2: Protein | Mass: 54042.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR1*PLUS #3: Protein | Mass: 48763.777 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR7*PLUS #4: Protein | Mass: 38118.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR8*PLUS #7: Protein | Mass: 7170.506 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P19052*PLUS #8: Protein/peptide | Mass: 4052.885 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P12240*PLUS #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: Q7DGD4 #10: Protein/peptide | Mass: 3891.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P19054*PLUS #11: Protein/peptide | Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P12241 #12: Protein/peptide | Mass: 4015.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P12312*PLUS #13: Protein | Mass: 26452.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR2*PLUS #14: Protein/peptide | Mass: 3620.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P12313 #15: Protein | Mass: 11095.432 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P56152*PLUS #17: Protein/peptide | Mass: 3477.162 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR4*PLUS #18: Protein/peptide | Mass: 2999.790 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR3*PLUS #19: Protein/peptide | Mass: 1975.426 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane #20: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: D0VWR5*PLUS |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9477.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P12238 #6: Protein/peptide | Mass: 4936.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermosynechococcus vulcanus (bacteria) / Cellular location: thylakoid membrane / References: UniProt: P12239 |
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-Sugars , 1 types, 8 molecules
#29: Sugar | ChemComp-DGD / |
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-Non-polymers , 10 types, 128 molecules
#21: Chemical | #22: Chemical | ChemComp-CLA / #23: Chemical | ChemComp-PHO / #24: Chemical | ChemComp-PQ9 / #25: Chemical | ChemComp-BCR / #26: Chemical | #27: Chemical | ChemComp-IOD / #28: Chemical | ChemComp-MGE / ( #30: Chemical | #31: Chemical | ChemComp-HEM / |
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-Details
Compound details | THIS ENTRY IS PHOTOSYSTENonpolymer details | CHLORIDE IONS LOCATED IN THE OXYGEN-EVOLVING CENTER WERE SUBSTITUTE | Sequence details | THERE IS NO DATABASE REFERENCE FOR CHAINS B,C,D,H,K,M,O,U,Y, X, AND Z AT THE TIME OF PROCESSING. ...THERE IS NO DATABASE REFERENCE FOR CHAINS B,C,D,H,K,M,O,U,Y, X, AND Z AT THE TIME OF PROCESSING | |
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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: 3.76 Å3/Da / Density % sol: 67.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 4% PEG 1450, 40mM MgSO4, 10mM MgCl2, 13% glycerol, 0.01% DM, 20mM MES (pH6.0), 10mM NaI, 5mM CaI, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2007 |
Radiation | Monochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 4→50 Å / Num. all: 75277 / Num. obs: 75277 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 25.57 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.158 / Num. unique all: 7447 / Rsym value: 0.908 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AXT Resolution: 4→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 7949177.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 84.842 Å2 / ksol: 0.25 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 164.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 4→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4→4.25 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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