+Open data
-Basic information
Entry | Database: PDB / ID: 5gij | |||||||||
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Title | Crystal structure of TDR-TDIF complex | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / LRR / TDR / TDIF / PXY / LRR-RK | |||||||||
Function / homology | Function and homology information procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / cell-cell signaling involved in cell fate commitment / phloem or xylem histogenesis / secondary shoot formation / apoplast / receptor serine/threonine kinase binding ...procambium histogenesis / phloem development / xylem development / axillary shoot meristem initiation / maintenance of root meristem identity / cell-cell signaling involved in cell fate commitment / phloem or xylem histogenesis / secondary shoot formation / apoplast / receptor serine/threonine kinase binding / regulation of cell differentiation / non-specific serine/threonine protein kinase / cell division / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Morita, J. / Kato, K. / Ishitani, R. / Nishimasu, H. / Nureki, O. | |||||||||
Citation | Journal: Nat Commun / Year: 2016 Title: Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide Authors: Morita, J. / Kato, K. / Nakane, T. / Kondo, Y. / Fukuda, H. / Nishimasu, H. / Ishitani, R. / Nureki, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gij.cif.gz | 141.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gij.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 5gij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/5gij ftp://data.pdbj.org/pub/pdb/validation_reports/gi/5gij | HTTPS FTP |
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-Related structure data
Related structure data | 4mnaS 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
-Protein / Protein/peptide , 2 types, 2 molecules BD
#1: Protein | Mass: 66735.195 Da / Num. of mol.: 1 / Fragment: extracellular domain, UNP residues 31-631 / Mutation: C259A, C540S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TDR, PXY, At5g61480, MCI2.4 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9FII5, non-specific serine/threonine protein kinase |
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#2: Protein/peptide | Mass: 1280.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Arabidopsis thaliana (thale cress) / References: UniProt: Q84W98 |
-Sugars , 5 types, 11 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||
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#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: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #7: 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: 8.62 Å3/Da / Density % sol: 85.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 4M sodium nitrate, 0.1M sodium acetate trihydrate, pH 4.8, 200mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→102.93 Å / Num. obs: 47698 / % possible obs: 99.8 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 3→3.11 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MNA Resolution: 3→57.556 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.88 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.97 Å2 / Biso mean: 76.1127 Å2 / Biso min: 45.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→57.556 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17
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