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- PDB-7djm: Structure of four truncated and mutated forms of quenching protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 7djm | |||||||||||||||||||||
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Title | Structure of four truncated and mutated forms of quenching protein | |||||||||||||||||||||
![]() | Protein SUPPRESSOR OF QUENCHING 1, chloroplastic | |||||||||||||||||||||
![]() | PLANT PROTEIN / Suppressor / Quenching | |||||||||||||||||||||
Function / homology | ![]() nonphotochemical quenching / thylakoid membrane / chloroplast thylakoid / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / hydrolase activity / nucleus / metal ion binding Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Yu, G.M. / Pan, X.W. / Li, M. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Arabidopsis SOQ1 lumenal region unveils C-terminal domain essential for negative regulation of photoprotective qH. Authors: Yu, G. / Hao, J. / Pan, X. / Shi, L. / Zhang, Y. / Wang, J. / Fan, H. / Xiao, Y. / Yang, F. / Lou, J. / Chang, W. / Malnoe, A. / Li, M. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.4 KB | Display | ![]() |
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PDB format | ![]() | 82.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7djjSC ![]() 7djkC ![]() 7djlC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 54123.477 Da / Num. of mol.: 1 / Fragment: NHL_CTD Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q8VZ10, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-DTT / | #4: Chemical | ChemComp-NA / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.32 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 25-34% PEG 3350, 0.2 M NH4Ac, 0.1M MES, pH 5.9-6.6 / PH range: 5.9-6.6 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9777 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 49848 / % possible obs: 99.8 % / Redundancy: 12.4 % / Biso Wilson estimate: 22.0080859116 Å2 / Rrim(I) all: 0.082 / Net I/σ(I): 33.36 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 2367 / CC1/2: 0.864 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DJJ Resolution: 1.70000117792→39.375 Å / SU ML: 0.167139620693 / Cross valid method: FREE R-VALUE / σ(F): 1.36333929852 / Phase error: 19.4162754482 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.9819224725 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.70000117792→39.375 Å
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Refine LS restraints |
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LS refinement shell |
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