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Open data
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Basic information
Entry | Database: PDB / ID: 5h2f | ||||||||||||
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Title | Crystal structure of the PsbM-deletion mutant of photosystem II | ||||||||||||
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![]() | PHOTOSYNTHESIS / Photosystem II / Mutant / PsbM | ||||||||||||
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 | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Uto, S. / Kawakami, K. / Umena, Y. / Iwai, M. / Ikeuchi, M. / Shen, J.R. / Kamiya, N. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Mutual relationships between structural and functional changes in a PsbM-deletion mutant of photosystem II. Authors: Uto, S. / Kawakami, K. / Umena, Y. / Iwai, M. / Ikeuchi, M. / Shen, J.R. / Kamiya, N. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1.1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 34.5 MB | Display | ![]() |
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Full document | ![]() | 35.4 MB | Display | |
Data in XML | ![]() | 298 KB | Display | |
Data in CIF | ![]() | 379.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3wu2S S: Starting model for refinement |
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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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Components
-Photosystem II ... , 15 types, 30 molecules AaBbCcDdHhIiJjKkLlOoTtUuYyXxZz
#1: Protein | Mass: 37059.258 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 11-344 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A444, photosystem II #2: Protein | Mass: 56096.758 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-506 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #3: Protein | Mass: 49668.758 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 7-461 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIF8 #4: Protein | Mass: 38404.949 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 11-352 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8CM25, photosystem II #7: Protein | Mass: 7057.349 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-64 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DJ43 #8: Protein/peptide | Mass: 4195.983 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-36 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein/peptide | Mass: 4105.908 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-40 / 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) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1K9 #11: Protein/peptide | Mass: 4038.735 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-37 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN8 #12: Protein | Mass: 26523.578 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-272 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A431 #13: Protein/peptide | Mass: 3648.379 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-30 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | Mass: 10966.317 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 38-134 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1L5 #16: Protein/peptide | Mass: 3098.921 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 18-46 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DJI1 #17: Protein/peptide | Mass: 3833.601 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-38 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q9F1R6 #18: Protein | Mass: 6766.187 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DHJ2 |
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-Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf
#5: Protein | Mass: 9220.409 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 5-84 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein/peptide | Mass: 3781.534 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 13-45 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: Q8DIN9 |
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-Protein , 1 types, 2 molecules Vv
#15: Protein | Mass: 15148.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: BP-1 / References: UniProt: P0A386 |
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-Sugars , 3 types, 38 molecules ![](data/chem/img/LMT.gif)
![](data/chem/img/HTG.gif)
![](data/chem/img/DGD.gif)
![](data/chem/img/HTG.gif)
![](data/chem/img/DGD.gif)
#29: Sugar | ChemComp-LMT / #34: Sugar | ChemComp-HTG / #35: Sugar | ChemComp-DGD / |
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-Non-polymers , 19 types, 2630 molecules ![](data/chem/img/OEX.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PHO.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/PL9.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/SQD.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/BCT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RRX.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/HOH.gif)
#19: Chemical | #20: Chemical | #21: Chemical | ChemComp-CL / #22: Chemical | ChemComp-CLA / #23: Chemical | ChemComp-PHO / #24: Chemical | ChemComp-BCR / #25: Chemical | ChemComp-LMG / #26: Chemical | ChemComp-PL9 / #27: Chemical | ChemComp-LHG / #28: Chemical | ChemComp-SQD / #30: Chemical | ChemComp-UNL / Num. of mol.: 27 / Source method: obtained synthetically #31: Chemical | ChemComp-DMS / #32: Chemical | #33: Chemical | ChemComp-CA / #36: Chemical | #37: Chemical | #38: Chemical | ChemComp-MG / #39: Chemical | #40: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.31 % |
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Crystal grow | Temperature: 285 K / Method: microbatch / pH: 6.1 Details: PEG1450, sodium chloride, calcium chloride, magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→50 Å / Num. all: 385629 / Num. obs: 385629 / % possible obs: 96.7 % / Redundancy: 5.2 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.092 / Rsym value: 0.083 / Net I/av σ(I): 8.331 / Net I/σ(I): 13.6 / Num. measured all: 2003997 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WU2 Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.768 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.97 Å2 / Biso mean: 42.025 Å2 / Biso min: 14.65 Å2
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Refinement step | Cycle: final / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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