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Yorodumi- PDB-8dpa: Crystal structure of the homodimeric AvrM14-B Nudix hydrolase eff... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dpa | |||||||||
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Title | Crystal structure of the homodimeric AvrM14-B Nudix hydrolase effector from Melampsora lini | |||||||||
Components | AvrM14-B | |||||||||
Keywords | HYDROLASE / Nudix hydrolase / Effector / mRNA decapping enzyme | |||||||||
Function / homology | NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / AvrM14-B Function and homology information | |||||||||
Biological species | Melampsora lini (flax rust) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | |||||||||
Authors | McCombe, C.L. / Outram, M.A. / Ericsson, D.J. / Williams, S.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: New Phytol. / Year: 2023 Title: A rust-fungus Nudix hydrolase effector decaps mRNA in vitro and interferes with plant immune pathways. Authors: McCombe, C.L. / Catanzariti, A.M. / Greenwood, J.R. / Desai, A.M. / Outram, M.A. / Yu, D.S. / Ericsson, D.J. / Brenner, S.E. / Dodds, P.N. / Kobe, B. / Jones, D.A. / Williams, S.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dpa.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dpa.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8dpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/8dpa ftp://data.pdbj.org/pub/pdb/validation_reports/dp/8dpa | HTTPS FTP |
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-Related structure data
Related structure data | 8dp8C 8dp9C C: citing same article (ref.) |
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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: 16659.744 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Melampsora lini (flax rust) / Gene: AvrM14 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B2CW14 #2: Chemical | #3: 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: 4.8 Å3/Da / Density % sol: 74.39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.8 M Ammonium sulphate 0.1 M Sodium acetate pH 4.2 - 4.4 0.1 M Magnesium chloride PH range: 4.2 - 4.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.839→35.63 Å / Num. obs: 57219 / % possible obs: 99.54 % / Redundancy: 11 % / Biso Wilson estimate: 35.82 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08854 / Rpim(I) all: 0.02773 / Rrim(I) all: 0.09289 / Net I/σ(I): 16.34 |
Reflection shell | Resolution: 1.839→1.905 Å / Redundancy: 10.8 % / Mean I/σ(I) obs: 0.84 / Num. unique obs: 5572 / CC1/2: 0.484 / CC star: 0.808 / % possible all: 96.36 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: AvrM14-B Monomer Resolution: 1.84→35.63 Å / SU ML: 0.2292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.5523 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: 48.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→35.63 Å
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Refine LS restraints |
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LS refinement shell |
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