+Open data
-Basic information
Entry | Database: PDB / ID: 6qwn | |||||||||
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Title | Protein peptide complex | |||||||||
Components |
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Keywords | PLANT PROTEIN / Leucine rich extensin / peptide signaling / cell wall signaling / LRR | |||||||||
Function / homology | Function and homology information regulation of pollen tube growth / pollen tube growth / structural constituent of cell wall / plasmodesma / apoplast / calcium-mediated signaling / hormone activity / cell wall organization / cell-cell signaling / extracellular region Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.892 Å | |||||||||
Authors | Moussu, S. / Caroline, C. / Santos-Fernandez, G. / Wehrle, S. / Grossniklaus, U. / Santiago, J. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2020 Title: Structural basis for recognition of RALF peptides by LRX proteins during pollen tube growth. Authors: Moussu, S. / Broyart, C. / Santos-Fernandez, G. / Augustin, S. / Wehrle, S. / Grossniklaus, U. / Santiago, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qwn.cif.gz | 382.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qwn.ent.gz | 311.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qwn_validation.pdf.gz | 868.6 KB | Display | wwPDB validaton report |
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Full document | 6qwn_full_validation.pdf.gz | 910.2 KB | Display | |
Data in XML | 6qwn_validation.xml.gz | 69.6 KB | Display | |
Data in CIF | 6qwn_validation.cif.gz | 91.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/6qwn ftp://data.pdbj.org/pub/pdb/validation_reports/qw/6qwn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
-Protein , 2 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 41765.914 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: pollen / Cell: pollen / Gene: PEX1, At3g19020, K13E13.23 / Plasmid: pACEBac1 / Cell (production host): pollen / Cell line (production host): TNAO38 / Organ (production host): pollen / Production host: Trichoplusia ni (cabbage looper) / Tissue (production host): pollen / References: UniProt: Q9LJ64 #2: Protein | Mass: 6817.940 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: pollen / Cell: pollen / Gene: RALFL4, At1g28270, F3H9.8 / Plasmid: pACEBac1 / Cell (production host): pollen / Cell line (production host): TNAO38 / Organ (production host): pollen / Production host: Trichoplusia ni (cabbage looper) / Tissue (production host): pollen / References: UniProt: Q9FZA0 |
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-Sugars , 6 types, 8 molecules
#3: 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)-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-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: 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 |
#7: 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 |
#8: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.34 % / Description: Elongated three dimensional needle |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 17.5% (w/v) PEG 8000, 0.1 M Bis-Tris pH7, 0.2 M sodium citrate PH range: ph 7 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999871 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 27, 2018 |
Radiation | Monochromator: Fixed-exit LN2 cooled Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999871 Å / Relative weight: 1 |
Reflection | Resolution: 3.892→49.44 Å / Num. obs: 28176 / % possible obs: 99.6 % / Observed criterion σ(I): 0.95 / Redundancy: 6.7 % / Biso Wilson estimate: 110.49 Å2 / CC1/2: 0.978 / Rrim(I) all: 0.495 / Rsym value: 0.457 / Net I/σ(I): 4.44 |
Reflection shell | Resolution: 3.892→4.13 Å / Redundancy: 6.71 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 4482 / CC1/2: 0.34 / Rrim(I) all: 2.26 / Rsym value: 2.092 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: LRX2 Resolution: 3.892→49.44 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.68
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.892→49.44 Å
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Refine LS restraints |
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LS refinement shell |
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