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- PDB-7ywf: Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ywf | |||||||||
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Title | Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain with bound galactobiose | |||||||||
![]() | Dirigent protein | |||||||||
![]() | PLANT PROTEIN / Monocot chimeric jacalin / Dirigent protein / Lectin / Pathogen resistance | |||||||||
Function / homology | ![]() phenylpropanoid biosynthetic process / apoplast / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Huwa, N. / Classen, T. / Weiergraeber, O.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The Crystal Structure of the Defense Conferring Rice Protein Os JAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain. Authors: Huwa, N. / Weiergraber, O.H. / Fejzagic, A.V. / Kirsch, C. / Schaffrath, U. / Classen, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.2 KB | Display | ![]() |
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PDB format | ![]() | 140.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 10.5 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r5zC ![]() 7yweC ![]() 7ywgC ![]() 7ywwC ![]() 6oodS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
-Protein / Sugars , 2 types, 6 molecules ABC
#1: Protein | Mass: 17452.025 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Polysaccharide | |
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-Non-polymers , 4 types, 8 molecules ![](data/chem/img/TRS.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DTU.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/DTU.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-TRS / |
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#4: Chemical | ChemComp-PO4 / |
#5: Chemical | ChemComp-DTU / ( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: ammonium dihydrogen phosphate, Tris-HCl, methylpentanediol, dithiothreitol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7749 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→45.9 Å / Num. obs: 13939 / % possible obs: 99.9 % / Redundancy: 5.73 % / Biso Wilson estimate: 86.52 Å2 / CC1/2: 0.995 / Net I/σ(I): 6.02 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 5.78 % / Mean I/σ(I) obs: 0.51 / Num. unique obs: 1029 / CC1/2: 0.381 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OOD Resolution: 2.6→45.9 Å / SU ML: 0.6254 / Cross valid method: FREE R-VALUE / Phase error: 42.7598 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 111.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→45.9 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 | Refine-ID: X-RAY DIFFRACTION
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