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Yorodumi- PDB-5y96: Crystal structure of ANXUR1 extracellular domain from Arabidopsis... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y96 | |||||||||
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Title | Crystal structure of ANXUR1 extracellular domain from Arabidopsis thaliana | |||||||||
Components | (Receptor-like protein kinase ANXUR1) x 2 | |||||||||
Keywords | TRANSFERASE / receptor-like kinase | |||||||||
Function / homology | Function and homology information pollen tube tip / transmembrane receptor protein tyrosine kinase activity / non-specific serine/threonine protein kinase / apical plasma membrane / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Du, S. / Xiao, J.Y. | |||||||||
Citation | Journal: Protein Sci. / Year: 2018 Title: Crystal structures of the extracellular domains of the CrRLK1L receptor-like kinases ANXUR1 and ANXUR2 Authors: Du, S. / Qu, L.J. / Xiao, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y96.cif.gz | 335 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y96.ent.gz | 268.9 KB | Display | PDB format |
PDBx/mmJSON format | 5y96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5y96_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5y96_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5y96_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 5y96_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/5y96 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/5y96 | HTTPS FTP |
-Related structure data
Related structure data | 5y92SC 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: 42835.949 Da / Num. of mol.: 1 / Fragment: UNP residues 27-40 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX1, At3g04690, F7O18.16 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9SR05, non-specific serine/threonine protein kinase | ||||
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#2: Protein | Mass: 42707.820 Da / Num. of mol.: 1 / Fragment: UNP residues 28-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ANX1, At3g04690, F7O18.16 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9SR05, non-specific serine/threonine protein kinase | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M Ammonium acetate,0.1M HEPES pH 7.5,25%(w/v) Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 83947 / % possible obs: 96.5 % / Redundancy: 3.5 % / Net I/σ(I): 17.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y92 Resolution: 1.8→43.339 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 23.68 / 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: 1.8→43.339 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: -20.7447 Å / Origin y: -108.3115 Å / Origin z: -156.5416 Å
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Refinement TLS group | Selection details: all |