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Yorodumi- PDB-7yww: Monocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yww | |||||||||
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Title | Monocot chimeric jacalin JAC1 from Oryza sativa: lectin domain (crystal form 2) | |||||||||
Components | Dirigent protein | |||||||||
Keywords | PLANT PROTEIN / Monocot chimeric jacalin / Dirigent protein / Lectin / Pathogen resistance | |||||||||
Function / homology | Function and homology information phenylpropanoid biosynthetic process / apoplast / carbohydrate binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Oryza sativa (Asian cultivated rice) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Huwa, N. / Classen, T. / Weiergraeber, O.H. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Biomolecules / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yww.cif.gz | 157.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yww.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 7yww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yww_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 7yww_full_validation.pdf.gz | 451.2 KB | Display | |
Data in XML | 7yww_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 7yww_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yw/7yww ftp://data.pdbj.org/pub/pdb/validation_reports/yw/7yww | HTTPS FTP |
-Related structure data
Related structure data | 7r5zC 7yweC 7ywfC 7ywgC 4pifS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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
#1: Protein | Mass: 18620.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: JAC1, LOC_Os12g14440, Os12g0247700, OSNPB_120247700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q306J3 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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