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Yorodumi- PDB-4yzh: Structure of the Arabidopsis TAP38/PPH1 in complex with pLhcb1 ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yzh | |||||||||
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Title | Structure of the Arabidopsis TAP38/PPH1 in complex with pLhcb1 phosphopeptide substrate | |||||||||
Components |
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Keywords | HYDROLASE/HYDROLASE SUBSTRATE / State transition / photosynthesis / PP2C phosphatase / phosphopeptide / HYDROLASE-HYDROLASE SUBSTRATE complex | |||||||||
Function / homology | Function and homology information photosystem stoichiometry adjustment / photosynthesis, light harvesting / response to fructose / thylakoid / apoplast / photosystem I / photosynthetic electron transport chain / photosystem II / chloroplast stroma / myosin phosphatase activity ...photosystem stoichiometry adjustment / photosynthesis, light harvesting / response to fructose / thylakoid / apoplast / photosystem I / photosynthetic electron transport chain / photosystem II / chloroplast stroma / myosin phosphatase activity / chlorophyll binding / protein-serine/threonine phosphatase / dephosphorylation / phosphatase activity / chloroplast thylakoid membrane / protein dephosphorylation / chloroplast / manganese ion binding / mRNA binding / nucleolus / magnesium ion binding / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Wei, X.P. / Guo, J.T. / Li, M. / Liu, Z.F. | |||||||||
Funding support | China, 2items
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Citation | Journal: Plant Cell / Year: 2015 Title: Structural Mechanism Underlying the Specific Recognition between the Arabidopsis State-Transition Phosphatase TAP38/PPH1 and Phosphorylated Light-Harvesting Complex Protein Lhcb1 Authors: Wei, X. / Guo, J. / Li, M. / Liu, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yzh.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yzh.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yzh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/4yzh ftp://data.pdbj.org/pub/pdb/validation_reports/yz/4yzh | HTTPS FTP |
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-Related structure data
Related structure data | 4yzgSC S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 33723.887 Da / Num. of mol.: 1 / Fragment: UNP residues 59-351 / Mutation: D180E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PPH1, At4g27800, T27E11.40 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P49599, protein-serine/threonine phosphatase | ||
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#2: Protein/peptide | Mass: 1679.854 Da / Num. of mol.: 1 / Fragment: UNP residues 36-50 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: P0CJ48 | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % Description: Thin plates with size of 0.2 mm x 0.1 mm x 0.02 mm |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG3350, 0.2 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 27032 / Num. obs: 27032 / % possible obs: 99.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.482 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4YZG Resolution: 2→38.505 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.505 Å
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Refine LS restraints |
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LS refinement shell |
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