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- PDB-7yww: Monocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yww | |||||||||
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Title | Monocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (crystal form 2) | |||||||||
![]() | 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 | ![]() | 157.4 KB | Display | ![]() |
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PDB format | ![]() | 108.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.7 KB | Display | ![]() |
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Full document | ![]() | 451.2 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7r5zC ![]() 7yweC ![]() 7ywfC ![]() 7ywgC ![]() 4pifS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18620.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-1PE / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: PEG 3350, ammonium iodide, potassium phosphate, N-acetylgalactosamine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→52.02 Å / Num. obs: 71961 / % possible obs: 97.2 % / Redundancy: 3.74 % / Biso Wilson estimate: 22.35 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.65 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 3.74 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 5441 / CC1/2: 0.501 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4PIF Resolution: 1.4→46.87 Å / SU ML: 0.2402 / Cross valid method: FREE R-VALUE / Phase error: 24.4977 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: 29.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→46.87 Å
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Refine LS restraints |
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LS refinement shell |
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