[English] 日本語
Yorodumi- PDB-7z1q: X-ray crystal structure of SLPYL1-E151D mutant with NIO molecules -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z1q | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystal structure of SLPYL1-E151D mutant with NIO molecules | ||||||
Components | SlPYL1-E151D | ||||||
Keywords | PLANT PROTEIN / SLPYL1 / ABA receptor protein | ||||||
Function / homology | Function and homology information abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / signaling receptor activity / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Solanum lycopersicum (tomato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.683 Å | ||||||
Authors | Infantes, L. / Albert, A. | ||||||
Funding support | Spain, 1items
| ||||||
Citation | Journal: Front Plant Sci / Year: 2022 Title: Structure-Based Modulation of the Ligand Sensitivity of a Tomato Dimeric Abscisic Acid Receptor Through a Glu to Asp Mutation in the Latch Loop. Authors: Infantes, L. / Rivera-Moreno, M. / Daniel-Mozo, M. / Benavente, J.L. / Ocana-Cuesta, J. / Coego, A. / Lozano-Juste, J. / Rodriguez, P.L. / Albert, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7z1q.cif.gz | 112.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7z1q.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 7z1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z1q_validation.pdf.gz | 988 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7z1q_full_validation.pdf.gz | 988.2 KB | Display | |
Data in XML | 7z1q_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 7z1q_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z1/7z1q ftp://data.pdbj.org/pub/pdb/validation_reports/z1/7z1q | HTTPS FTP |
-Related structure data
Related structure data | 7z1pC 7z1rC 7z1sC 5moaS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25724.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum lycopersicum (tomato) / Gene: 101268417 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q7HTY9 | ||||||||
---|---|---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.58 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Ammonium sulfate 1.8M |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Synchrotron / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 5, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.683→44.6 Å / Num. obs: 27741 / % possible obs: 99.84 % / Redundancy: 9.8 % / Biso Wilson estimate: 29.25 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04322 / Rpim(I) all: 0.01428 / Rrim(I) all: 0.04557 / Net I/σ(I): 31.29 |
Reflection shell | Resolution: 1.683→1.744 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.9637 / Mean I/σ(I) obs: 1.91 / Num. unique obs: 2726 / CC1/2: 0.79 / CC star: 0.939 / Rpim(I) all: 0.3954 / Rrim(I) all: 1.045 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MOA Resolution: 1.683→44.6 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.9899 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.683→44.6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
|