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Yorodumi- PDB-7djk: Structure of four truncated and mutated forms of quenching protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 7djk | |||||||||||||||||||||
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Title | Structure of four truncated and mutated forms of quenching protein | |||||||||||||||||||||
Components | Protein SUPPRESSOR OF QUENCHING 1, chloroplastic | |||||||||||||||||||||
Keywords | PLANT PROTEIN / Suppressor / Quenching | |||||||||||||||||||||
Function / homology | Function and homology information nonphotochemical quenching / thylakoid membrane / chloroplast thylakoid / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / chloroplast stroma / chloroplast thylakoid membrane / chloroplast / hydrolase activity / metal ion binding / nucleus Similarity search - Function | |||||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80145117414 Å | |||||||||||||||||||||
Authors | Yu, G.M. / Pan, X.W. / Li, M. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Nat.Plants / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7djk.cif.gz | 247.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7djk.ent.gz | 173.8 KB | Display | PDB format |
PDBx/mmJSON format | 7djk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/7djk ftp://data.pdbj.org/pub/pdb/validation_reports/dj/7djk | HTTPS FTP |
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-Related structure data
Related structure data | 7djjC 7djlC 7djmC 6gc1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 73224.172 Da / Num. of mol.: 1 / Fragment: Trx_NHL / Mutation: C430S,C431S,C434S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOQ1, At1g56500, F13N6.21 / Production host: Komagataella pastoris (fungus) References: UniProt: Q8VZ10, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.48 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M NaCl, 0.1 M tri-Sodium citrate pH 5.6, 12% (w/v) polyethylene glycol 4000 (PEG 4000) |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 25154 / % possible obs: 98.53 % / Redundancy: 5.2 % / Biso Wilson estimate: 42.7055086191 Å2 / Rpim(I) all: 0.05 / Net I/σ(I): 12.13 |
Reflection shell | Resolution: 2.8→2.85 Å / Num. unique obs: 1241 / CC1/2: 0.79 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6GC1 Resolution: 2.80145117414→46.8396000193 Å / SU ML: 0.238091856452 / Cross valid method: FREE R-VALUE / σ(F): 1.34361293242 / Phase error: 20.8852629862 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: 45.7388519777 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.80145117414→46.8396000193 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 203.987218744 Å / Origin y: 49.519451362 Å / Origin z: 52.5107330499 Å
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Refinement TLS group | Selection details: all |