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- PDB-8dpa: Crystal structure of the homodimeric AvrM14-B Nudix hydrolase eff... -

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Basic information

Entry
Database: PDB / ID: 8dpa
TitleCrystal structure of the homodimeric AvrM14-B Nudix hydrolase effector from Melampsora lini
ComponentsAvrM14-B
KeywordsHYDROLASE / Nudix hydrolase / Effector / mRNA decapping enzyme
Function / homologyNUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / AvrM14-B
Function and homology information
Biological speciesMelampsora lini (flax rust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMcCombe, C.L. / Outram, M.A. / Ericsson, D.J. / Williams, S.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100893 Australia
Australian Research Council (ARC)FT200100135 Australia
CitationJournal: 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
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AvrM14-B
B: AvrM14-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6085
Polymers33,3192
Non-polymers2883
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7840 Å2
ΔGint-82 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.663, 79.663, 201.317
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-354-

HOH

21A-361-

HOH

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Components

#1: Protein AvrM14-B


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 ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.8 Å3/Da / Density % sol: 74.39 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
Cootmodel building
PHENIX1.19_4092model building
XDSdata reduction
Aimlessdata scaling
PHASER1.19_4092phasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2215 2832 4.97 %
Rwork0.1896 54206 -
obs0.1912 57038 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.37 Å2
Refinement stepCycle: LAST / Resolution: 1.84→35.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 15 126 2264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972200
X-RAY DIFFRACTIONf_angle_d0.9592967
X-RAY DIFFRACTIONf_chiral_restr0.066318
X-RAY DIFFRACTIONf_plane_restr0.009386
X-RAY DIFFRACTIONf_dihedral_angle_d16.5985832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.42171360.34912461X-RAY DIFFRACTION92.82
1.87-1.90.33691360.30512693X-RAY DIFFRACTION99.86
1.9-1.940.30891270.27282687X-RAY DIFFRACTION99.79
1.94-1.980.27661340.24822656X-RAY DIFFRACTION99.75
1.98-2.020.28551390.23222678X-RAY DIFFRACTION99.86
2.02-2.070.26321550.21882665X-RAY DIFFRACTION99.93
2.07-2.120.26871400.22332683X-RAY DIFFRACTION99.96
2.12-2.180.26161440.19052671X-RAY DIFFRACTION100
2.18-2.240.21851380.16612689X-RAY DIFFRACTION99.96
2.24-2.320.20361280.1562707X-RAY DIFFRACTION99.86
2.32-2.40.18131630.16172693X-RAY DIFFRACTION99.96
2.4-2.50.20851470.15692693X-RAY DIFFRACTION99.93
2.5-2.610.17771310.16382701X-RAY DIFFRACTION99.96
2.61-2.750.21791440.17782741X-RAY DIFFRACTION99.93
2.75-2.920.22081380.18942723X-RAY DIFFRACTION100
2.92-3.140.21381270.18912737X-RAY DIFFRACTION99.97
3.14-3.460.2381610.1922749X-RAY DIFFRACTION99.97
3.46-3.960.19961470.17142769X-RAY DIFFRACTION100
3.96-4.990.19641400.16232832X-RAY DIFFRACTION100
4.99-35.630.23221570.22192978X-RAY DIFFRACTION99.71

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