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- PDB-8sxs: Crystal structure of a Nudix hydrolase effector from Magnaporthe ... -

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Basic information

Entry
Database: PDB / ID: 8sxs
TitleCrystal structure of a Nudix hydrolase effector from Magnaporthe oryzae
ComponentsNudix hydrolase domain-containing protein
KeywordsHYDROLASE / Nudix hydrolase / Effector / Inositol pyrophosphate hydrolase
Function / homologyNUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Nudix hydrolase domain-containing protein
Function and homology information
Biological speciesPyricularia oryzae 70-15 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsMcCombe, C.L. / Ericsson, D.J. / Williams, S.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100893 Australia
Australian Research Council (ARC)FT200100135 Australia
Citation
Journal: Science / Year: 2025
Title: Plant pathogenic fungi hijack phosphate signaling with conserved enzymatic effectors.
Authors: McCombe, C.L. / Wegner, A. / Wirtz, L. / Zamora, C.S. / Casanova, F. / Aditya, S. / Greenwood, J.R. / de Paula, S. / England, E. / Shang, S. / Ericsson, D.J. / Oliveira-Garcia, E. / ...Authors: McCombe, C.L. / Wegner, A. / Wirtz, L. / Zamora, C.S. / Casanova, F. / Aditya, S. / Greenwood, J.R. / de Paula, S. / England, E. / Shang, S. / Ericsson, D.J. / Oliveira-Garcia, E. / Williams, S.J. / Schaffrath, U.
#1: Journal: Biorxiv / Year: 2023
Title: Plant pathogenic fungi hijack phosphate starvation signaling with conserved enzymatic effectors
Authors: McCombe, C.L. / Wegner, A. / Zamora, C.S. / Casanova, F. / Aditya, S. / Greenwood, J.R. / Wirtz, L. / de Paula, S. / England, E. / Shang, S. / Ericsson, D.J. / Oliveira-Garcia, E. / ...Authors: McCombe, C.L. / Wegner, A. / Zamora, C.S. / Casanova, F. / Aditya, S. / Greenwood, J.R. / Wirtz, L. / de Paula, S. / England, E. / Shang, S. / Ericsson, D.J. / Oliveira-Garcia, E. / Williams, S.J. / Schaffrath, U.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionMay 23, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nudix hydrolase domain-containing protein
B: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)27,3852
Polymers27,3852
Non-polymers00
Water7,044391
1
A: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)13,6921
Polymers13,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nudix hydrolase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)13,6921
Polymers13,6921
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.188, 60.545, 62.492
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

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Components

#1: Protein Nudix hydrolase domain-containing protein / MoNudix


Mass: 13692.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyricularia oryzae 70-15 (fungus) / Gene: MGG_14156 / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: G5EH10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 391 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM Potassium thiocyanate 20% w/v PEG 3350

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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: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.57→43.5 Å / Num. obs: 32124 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.13 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.02 / Rrim(I) all: 0.051 / Net I/σ(I): 22.35
Reflection shellResolution: 1.57→1.62 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 5.9 / Num. unique obs: 3049 / CC1/2: 0.979 / Rpim(I) all: 0.089 / Rrim(I) all: 0.232 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→42.97 Å / SU ML: 0.114 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3949
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 1565 4.87 %
Rwork0.1558 30550 -
obs0.1577 32115 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.85 Å2
Refinement stepCycle: LAST / Resolution: 1.57→42.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 0 391 2315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092055
X-RAY DIFFRACTIONf_angle_d1.01782791
X-RAY DIFFRACTIONf_chiral_restr0.0584286
X-RAY DIFFRACTIONf_plane_restr0.0079367
X-RAY DIFFRACTIONf_dihedral_angle_d13.7294755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.620.22321610.16772600X-RAY DIFFRACTION96.17
1.62-1.670.16821700.16262701X-RAY DIFFRACTION99.86
1.67-1.740.18191680.15522725X-RAY DIFFRACTION99.93
1.74-1.820.19941350.15852763X-RAY DIFFRACTION99.76
1.82-1.920.21771280.15462773X-RAY DIFFRACTION100
1.92-2.040.18981320.15072782X-RAY DIFFRACTION100
2.04-2.190.18751590.14952766X-RAY DIFFRACTION99.9
2.19-2.410.19391210.14812794X-RAY DIFFRACTION99.9
2.41-2.760.15821000.15852845X-RAY DIFFRACTION99.93
2.76-3.480.18711320.15352850X-RAY DIFFRACTION99.9
3.48-42.970.21491590.16042951X-RAY DIFFRACTION99.71

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