+Open data
-Basic information
Entry | Database: PDB / ID: 4z64 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | the plant peptide hormone receptor complex in arabidopsis | |||||||||
Components |
| |||||||||
Keywords | HORMONE / hormone receptor complex | |||||||||
Function / homology | Function and homology information regulation of defense response / microsporogenesis / floral organ abscission / pollen maturation / peptide receptor activity / guanylate cyclase / brassinosteroid mediated signaling pathway / guanylate cyclase activity / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity ...regulation of defense response / microsporogenesis / floral organ abscission / pollen maturation / peptide receptor activity / guanylate cyclase / brassinosteroid mediated signaling pathway / guanylate cyclase activity / embryo development ending in seed dormancy / transmembrane receptor protein serine/threonine kinase activity / receptor serine/threonine kinase binding / Golgi organization / transmembrane receptor protein tyrosine kinase activity / receptor protein-tyrosine kinase / protein autophosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / signaling receptor binding / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / ATP binding / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) Arabidopsis (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.659 Å | |||||||||
Authors | Chai, J. / Wang, J. / Han, Z. | |||||||||
Citation | Journal: Nature / Year: 2015 Title: Allosteric receptor activation by the plant peptide hormone phytosulfokine Authors: Wang, J. / Li, H. / Han, Z. / Zhang, H. / Wang, T. / Lin, G. / Chang, J. / Yang, W. / Chai, J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4z64.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4z64.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/4z64 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/4z64 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4z5wSC 4z61C 4z62C 4z63C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 69884.008 Da / Num. of mol.: 1 / Fragment: UNP resides 24-648 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PSKR1, PSKR, At2g02220, F5O4.1 Production host: Insect cell expression vector pTIE1 (others) References: UniProt: Q9ZVR7, non-specific serine/threonine protein kinase |
---|---|
#2: Protein | Mass: 23981.150 Da / Num. of mol.: 1 / Fragment: UNP residues 1-213 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK1 / Production host: Insect BA phytoplasma (bacteria) References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase |
-Protein/peptide / Non-polymers , 2 types, 5 molecules P
#3: Protein/peptide | Mass: 846.879 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis (plant) |
---|---|
#6: Chemical | ChemComp-SO4 / |
-Sugars , 2 types, 10 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#5: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5 Å3/Da / Density % sol: 75.4 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate pH4.5, 2.0 M (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: BRUKER SMART 6500 / Detector: CCD / Date: Sep 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→99 Å / Num. obs: 49253 / % possible obs: 96.8 % / Redundancy: 4.2 % / Net I/σ(I): 15.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Z5W Resolution: 2.659→48.913 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 29.16 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.659→48.913 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -53.4774 Å / Origin y: -33.4835 Å / Origin z: -8.2839 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |