+Open data
-Basic information
Entry | Database: PDB / ID: 7mlc | ||||||
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Title | PYL10 bound to the ABA pan-antagonist 4a | ||||||
Components | Abscisic acid receptor PYL10 | ||||||
Keywords | PLANT PROTEIN/ANTAGONIST / PYR/PYL/RCAR / PYL10 / HORMONE RECEPTOR / PLANT PROTEIN / PLANT PROTEIN-ANTAGONIST complex | ||||||
Function / homology | Function and homology information : / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / protein homodimerization activity / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Peterson, F.C. / Vaidya, A.S. / Volkman, B.F. / Cutler, S.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Click-to-lead design of a picomolar ABA receptor antagonist with potent activity in vivo. Authors: Vaidya, A.S. / Peterson, F.C. / Eckhardt, J. / Xing, Z. / Park, S.Y. / Dejonghe, W. / Takeuchi, J. / Pri-Tal, O. / Faria, J. / Elzinga, D. / Volkman, B.F. / Todoroki, Y. / Mosquna, A. / ...Authors: Vaidya, A.S. / Peterson, F.C. / Eckhardt, J. / Xing, Z. / Park, S.Y. / Dejonghe, W. / Takeuchi, J. / Pri-Tal, O. / Faria, J. / Elzinga, D. / Volkman, B.F. / Todoroki, Y. / Mosquna, A. / Okamoto, M. / Cutler, S.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mlc.cif.gz | 97.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mlc.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 7mlc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mlc_validation.pdf.gz | 752.8 KB | Display | wwPDB validaton report |
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Full document | 7mlc_full_validation.pdf.gz | 753.6 KB | Display | |
Data in XML | 7mlc_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 7mlc_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/7mlc ftp://data.pdbj.org/pub/pdb/validation_reports/ml/7mlc | HTTPS FTP |
-Related structure data
Related structure data | 7mldC 6nwbS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 17747.307 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PYL10, RCAR4, At4g27920, T13J8.30 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8H1R0 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-ZLA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.06 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 200 mM tribasic ammonium citrate and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 15495 / % possible obs: 97 % / Redundancy: 6.8 % / Biso Wilson estimate: 26.28 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 1.77→1.83 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 5.4 / Num. unique obs: 1467 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.175 / Rrim(I) all: 0.423 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6NWB Resolution: 1.77→42.41 Å / SU ML: 0.207 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.7478 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: 32.13 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.77→42.41 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: -10.0174222345 Å / Origin y: -4.21542671743 Å / Origin z: 7.46642439494 Å
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Refinement TLS group | Selection details: (chain 'A' and resid 25 through 180) |