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- PDB-8dp9: Crystal structure of the monomeric AvrM14-B Nudix hydrolase effec... -

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Basic information

Entry
Database: PDB / ID: 8dp9
TitleCrystal structure of the monomeric 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: 1.76 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,8007
Polymers33,3192
Non-polymers4805
Water4,522251
1
A: AvrM14-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8523
Polymers16,6601
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AvrM14-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9484
Polymers16,6601
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.059, 80.059, 293.949
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-400-

HOH

21B-401-

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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 4.09 Å3/Da / Density % sol: 69.92 %
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: Feb 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.76→48.99 Å / Num. obs: 56341 / % possible obs: 99.9 % / Redundancy: 23 % / Biso Wilson estimate: 24.78 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.06828 / Rpim(I) all: 0.01452 / Rrim(I) all: 0.06984 / Net I/σ(I): 31.89
Reflection shellResolution: 1.761→1.839 Å / Redundancy: 23.4 % / Rmerge(I) obs: 0.7627 / Mean I/σ(I) obs: 4.18 / Num. unique obs: 5485 / CC1/2: 0.941 / CC star: 0.985 / Rpim(I) all: 0.159 / Rrim(I) all: 0.7795 / % possible all: 99

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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-A

Resolution: 1.76→44.84 Å / SU ML: 0.2076 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.6265
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2014 2822 5.01 %
Rwork0.1775 53511 -
obs0.1787 56333 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.8 Å2
Refinement stepCycle: LAST / Resolution: 1.76→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 25 251 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00892226
X-RAY DIFFRACTIONf_angle_d0.99313005
X-RAY DIFFRACTIONf_chiral_restr0.0668324
X-RAY DIFFRACTIONf_plane_restr0.0072387
X-RAY DIFFRACTIONf_dihedral_angle_d15.4589830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.37961340.31722559X-RAY DIFFRACTION98.07
1.79-1.820.32451420.25492648X-RAY DIFFRACTION99.96
1.82-1.860.28341210.20022619X-RAY DIFFRACTION100
1.86-1.90.18131090.16732637X-RAY DIFFRACTION100
1.9-1.940.22341470.14712606X-RAY DIFFRACTION99.82
1.94-1.980.17741580.14442609X-RAY DIFFRACTION99.96
1.98-2.030.18121460.14832620X-RAY DIFFRACTION100
2.03-2.090.1841430.1522620X-RAY DIFFRACTION100
2.09-2.150.19271410.16872642X-RAY DIFFRACTION100
2.15-2.220.22041530.1752644X-RAY DIFFRACTION100
2.22-2.30.19021490.15222632X-RAY DIFFRACTION100
2.3-2.390.20851290.15632677X-RAY DIFFRACTION100
2.39-2.50.19041400.16242678X-RAY DIFFRACTION99.96
2.5-2.630.18151630.16462617X-RAY DIFFRACTION100
2.63-2.80.20861420.17652692X-RAY DIFFRACTION100
2.8-3.010.2091390.1852707X-RAY DIFFRACTION100
3.01-3.310.17531280.18252745X-RAY DIFFRACTION100
3.31-3.790.17891460.16592734X-RAY DIFFRACTION100
3.79-4.780.16431450.16222801X-RAY DIFFRACTION100
4.78-44.840.26441470.22173024X-RAY DIFFRACTION100

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