+Open data
-Basic information
Entry | Database: PDB / ID: 5gqr | ||||||
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Title | Crystal structure of PXY-CLE41-SERK2 | ||||||
Components |
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Keywords | TRANSFERASE / Meristem cell proliferation / SERK / CLE peptides / leucine rich repeat | ||||||
Function / homology | Function and homology information procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / microsporogenesis / cell-cell signaling involved in cell fate commitment / pollen maturation / phloem or xylem histogenesis / secondary shoot formation ...procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / microsporogenesis / cell-cell signaling involved in cell fate commitment / pollen maturation / phloem or xylem histogenesis / secondary shoot formation / brassinosteroid mediated signaling pathway / apoplast / receptor serine/threonine kinase binding / regulation of cell differentiation / non-specific serine/threonine protein kinase / cell division / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / lipid binding / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) Arabideae (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Chai, J.J. / Zhang, H.Q. | ||||||
Citation | Journal: Mol Plant / Year: 2016 Title: SERK Family Receptor-like Kinases Function as Co-receptors with PXY for Plant Vascular Development Authors: Zhang, H.Q. / Lin, X.Y. / Han, Z.F. / Wang, J. / Qu, L.J. / Chai, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gqr.cif.gz | 320.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gqr.ent.gz | 264.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gqr_validation.pdf.gz | 479.5 KB | Display | wwPDB validaton report |
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Full document | 5gqr_full_validation.pdf.gz | 502.9 KB | Display | |
Data in XML | 5gqr_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 5gqr_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gq/5gqr ftp://data.pdbj.org/pub/pdb/validation_reports/gq/5gqr | HTTPS FTP |
-Related structure data
Related structure data | 4mn8S S: Starting model for refinement |
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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: 65853.289 Da / Num. of mol.: 1 / Fragment: UNP residues 32-629 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TDR / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9FII5, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1264.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabideae (plant) / References: UniProt: Q941C5*PLUS |
#3: Protein | Mass: 20191.816 Da / Num. of mol.: 1 / Fragment: UNP residues 30-214 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SERK2 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9XIC7, non-specific serine/threonine protein kinase |
#4: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 70.06 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Potassium chloride, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. obs: 18060 / % possible obs: 95.13 % / Redundancy: 4.3 % / Rsym value: 0.144 / Net I/σ(I): 6.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MN8 Resolution: 3.5→40.472 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.31 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→40.472 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: 58.0206 Å / Origin y: -31.857 Å / Origin z: 14.2508 Å
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Refinement TLS group | Selection details: all |