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Open data
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Basic information
| Entry | Database: PDB / ID: 7ogq | ||||||
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| Title | Plant peptide hormone receptor H1I2S1 | ||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN / Plant receptor LRR pepide hormone | ||||||
| Function / homology | Function and homology informationmicrosporogenesis / floral organ abscission / pollen maturation / brassinosteroid mediated signaling pathway / 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 ...microsporogenesis / floral organ abscission / pollen maturation / brassinosteroid mediated signaling pathway / 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 / protein phosphorylation / non-specific serine/threonine protein kinase / signaling receptor binding / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex / mitochondrion / extracellular region / ATP binding / identical protein binding / plasma membrane Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Roman, A.O. / Jimenez-Sandoval, P. / Santiago, J. | ||||||
| Funding support | Switzerland, 1items
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Citation | Journal: Nat Commun / Year: 2022Title: HSL1 and BAM1/2 impact epidermal cell development by sensing distinct signaling peptides. Authors: Roman, A.O. / Jimenez-Sandoval, P. / Augustin, S. / Broyart, C. / Hothorn, L.A. / Santiago, J. | ||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 7ogq.cif.gz | 317.9 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb7ogq.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 7ogq.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 7ogq_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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| Full document | 7ogq_full_validation.pdf.gz | 2.9 MB | Display | |
| Data in XML | 7ogq_validation.xml.gz | 33.6 KB | Display | |
| Data in CIF | 7ogq_validation.cif.gz | 48.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/7ogq ftp://data.pdbj.org/pub/pdb/validation_reports/og/7ogq | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 7odkC ![]() 7odvC ![]() 7ogoC ![]() 7oguC ![]() 7ogzC ![]() 5ixoS S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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| Unit cell |
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| Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AAABBB
| #1: Protein | Mass: 66569.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Trichoplusia ni (cabbage looper)References: UniProt: Q9SGP2, non-specific serine/threonine protein kinase |
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| #2: Protein | Mass: 21978.709 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Trichoplusia ni (cabbage looper)References: UniProt: Q94AG2, receptor protein-tyrosine kinase, non-specific serine/threonine protein kinase |
-Protein/peptide , 1 types, 1 molecules CCC
| #3: Protein/peptide | Mass: 1527.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() |
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-Sugars , 7 types, 13 molecules 
| #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)][alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||||||||
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| #5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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 #7: Polysaccharide | Source method: isolated from a genetically manipulated source #8: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...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 #9: Polysaccharide | Source method: isolated from a genetically manipulated source #10: Sugar | |
-Non-polymers , 2 types, 324 molecules 


| #11: Chemical | ChemComp-SO4 / #12: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | N |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.21 % |
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| Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2 M ammonium sulphate 0.1 M Bis-Tris 25 % w/v PEG 3350 |
-Data collection
| Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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| Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.254716 Å | |||||||||||||||||||||
| Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 21, 2020 | |||||||||||||||||||||
| Radiation | Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
| Radiation wavelength | Wavelength: 1.254716 Å / Relative weight: 1 | |||||||||||||||||||||
| Reflection | Resolution: 2.2→46.973 Å / Num. obs: 65575 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.047 / Rrim(I) all: 0.124 / Net I/σ(I): 14.5 | |||||||||||||||||||||
| Reflection shell | Diffraction-ID: 1
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 5IXO Resolution: 2.2→46.973 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.915 / SU B: 12.687 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.195 / ESU R Free: 0.173 Details: Hydrogens have been added in their riding positions
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| Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 53.542 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.2→46.973 Å
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| Refine LS restraints |
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| LS refinement shell |
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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About Yorodumi





X-RAY DIFFRACTION
Switzerland, 1items
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Trichoplusia ni (cabbage looper)