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- PDB-8dp8: Crystal structure of the monomeric AvrM14-A Nudix hydrolase effec... -

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Basic information

Entry
Database: PDB / ID: 8dp8
TitleCrystal structure of the monomeric AvrM14-A Nudix hydrolase effector from Melampsora lini
ComponentsAvrM14-A
KeywordsHYDROLASE / Nudix hydrolase / Effector / mRNA decapping enzyme
Function / homologyNUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / AvrM14-A
Function and homology information
Biological speciesMelampsora lini (flax rust)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.30001006071 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: AvrM14-A
A: AvrM14-A
C: AvrM14-A


Theoretical massNumber of molelcules
Total (without water)49,9343
Polymers49,9343
Non-polymers00
Water2,396133
1
B: AvrM14-A


Theoretical massNumber of molelcules
Total (without water)16,6451
Polymers16,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AvrM14-A


Theoretical massNumber of molelcules
Total (without water)16,6451
Polymers16,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AvrM14-A


Theoretical massNumber of molelcules
Total (without water)16,6451
Polymers16,6451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.645, 166.842, 62.911
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 38 and (name N or name...A38 - 39
121(chain A and ((resid 38 and (name N or name...A41 - 64
131(chain A and ((resid 38 and (name N or name...A72 - 103
141(chain A and ((resid 38 and (name N or name...A106 - 116
151(chain A and ((resid 38 and (name N or name...A124 - 135
161(chain A and ((resid 38 and (name N or name...A147
171(chain A and ((resid 38 and (name N or name...A149 - 154
181(chain A and ((resid 38 and (name N or name...A156 - 163
191(chain A and ((resid 38 and (name N or name...A166 - 179
2101(chain B and ((resid 38 and (name N or name...B38 - 39
2111(chain B and ((resid 38 and (name N or name...B41 - 64
2121(chain B and ((resid 38 and (name N or name...B72 - 103
2131(chain B and ((resid 38 and (name N or name...B106 - 116
2141(chain B and ((resid 38 and (name N or name...B124 - 135
2151(chain B and ((resid 38 and (name N or name...B147
2161(chain B and ((resid 38 and (name N or name...B149 - 154
2171(chain B and ((resid 38 and (name N or name...B156 - 163
2181(chain B and ((resid 38 and (name N or name...B166 - 179
3191(chain C and ((resid 38 and (name N or name...C38 - 39
3201(chain C and ((resid 38 and (name N or name...C41 - 64
3211(chain C and ((resid 38 and (name N or name...C72 - 103
3221(chain C and ((resid 38 and (name N or name...C106 - 116
3231(chain C and ((resid 38 and (name N or name...C124 - 135
3241(chain C and ((resid 38 and (name N or name...C147
3251(chain C and ((resid 38 and (name N or name...C149 - 154
3261(chain C and ((resid 38 and (name N or name...C156 - 163
3271(chain C and ((resid 38 and (name N or name...C166 - 179

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Components

#1: Protein AvrM14-A


Mass: 16644.754 Da / Num. of mol.: 3
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: A0A1B2CW89
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.4 M sodium malonate pH 6.0 2% Glycerol

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→41.7105 Å / Num. obs: 18412 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 29.5277484254 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.804 / Num. unique obs: 1793 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.30001006071→41.7105 Å / SU ML: 0.255124740033 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.7979767625
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25146218903 934 5.16250276365 %
Rwork0.183257954802 17158 -
obs0.186710724587 18092 98.2673401771 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.4806719878 Å2
Refinement stepCycle: LAST / Resolution: 2.30001006071→41.7105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3193 0 0 133 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007939912396093254
X-RAY DIFFRACTIONf_angle_d0.981956395734379
X-RAY DIFFRACTIONf_chiral_restr0.0615502135701479
X-RAY DIFFRACTIONf_plane_restr0.00636084327315564
X-RAY DIFFRACTIONf_dihedral_angle_d17.30981342421967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.301-2.42130.3115022841411240.224896854042350X-RAY DIFFRACTION96.0031043849
2.4213-2.57290.3126601482241510.2181106272122342X-RAY DIFFRACTION97.0038910506
2.5729-2.77160.2766095376081370.2190543615082393X-RAY DIFFRACTION98.2142857143
2.7716-3.05040.2817316956621290.2048161909252460X-RAY DIFFRACTION99.0815154994
3.0504-3.49160.2629106222341250.1843902230662495X-RAY DIFFRACTION99.430740038
3.4916-4.39830.21831780821320.1480213009952486X-RAY DIFFRACTION99.5437262357
4.3983-41.71050.2163471121361360.1720647189422632X-RAY DIFFRACTION98.5754985755
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.937897664180.017724567274-0.2763275973852.802113168380.6017088336661.357015157220.02759882872020.160833165520.0456187309691-0.1874361428520.003182065342770.0009225334920660.01757339258230.0383075480484-0.01335332071330.165674601344-0.0105998187849-0.01501376508980.2373752267020.006037121197060.17907011437-13.396366445628.4681751685-12.1519328591
21.494602426570.136240638246-0.3050125384153.165431278170.9075690362323.10753575583-0.0354421663560.04211944251470.0264141476567-0.317729973286-0.02613073409740.0576467424913-0.128661208744-0.1029246759650.02289736054940.131240103977-0.005518587953440.009961752802210.1802163637450.04276758679230.184437519112-14.163224131555.4990747038-12.7716615002
31.991420459240.574633056993-0.1997334713863.81188838125-0.1223171437592.038245534470.0310328387397-0.0850064565391-0.03430208198640.053008361397-0.0741339549445-0.07734250118370.2410582346070.0452623504430.03592556829840.1977852376160.0169872318296-0.02240614461580.1948040989940.03353345147310.193679452199-9.7886588434984.9222761708-22.1479946362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 37 through 179 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 179 )
3X-RAY DIFFRACTION3chain 'C' and (resid 37 through 179 )

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