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- PDB-8pq7: The Potato Late Blight pathogen (Phytophthora infestans) effector... -

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Basic information

Entry
Database: PDB / ID: 8pq7
TitleThe Potato Late Blight pathogen (Phytophthora infestans) effector protein Pi04134 in complex with potato protein phosphatase type 1c (PP1c).
Components
  • RxLR effector protein PexRD24
  • Serine/threonine-protein phosphatase
KeywordsPLANT PROTEIN / protein complex / plant pathogen interactions / effector protein / phosphatase
Function / homology
Function and homology information


host cell nucleoplasm / host cell nucleolus / myosin phosphatase activity / protein-serine/threonine phosphatase / extracellular region / metal ion binding
Similarity search - Function
RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 ...RXLR phytopathogen effector protein / RXLR phytopathogen effector protein, Avirulence activity / Serine-threonine protein phosphatase, N-terminal / : / Serine-threonine protein phosphatase N-terminal domain / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / RxLR effector protein PexRD24 / Serine/threonine-protein phosphatase
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
Phytophthora infestans (potato late blight agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBentham, A.R. / Banfield, M.J.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
John Innes Foundation United Kingdom
UK Research and Innovation (UKRI)BB/M011216/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012574 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9797 United Kingdom
CitationJournal: Mol.Plant Microbe Interact. / Year: 2024
Title: The WY Domain of an RxLr Effector Drives Interactions with a Host Target Phosphatase to Mimic Host Regulatory Proteins and Promote Phytophthora infestans Infection.
Authors: Bentham, A.R. / Wang, W. / Trusch, F. / Varden, F.A. / Birch, P.R.J. / Banfield, M.J.
History
DepositionJul 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source / pdbx_validate_planes
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_validate_planes.type
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase
B: RxLR effector protein PexRD24
C: Serine/threonine-protein phosphatase
D: RxLR effector protein PexRD24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,50811
Polymers88,1024
Non-polymers4067
Water3,801211
1
A: Serine/threonine-protein phosphatase
B: RxLR effector protein PexRD24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2235
Polymers44,0512
Non-polymers1723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-24 kcal/mol
Surface area16500 Å2
MethodPISA
2
C: Serine/threonine-protein phosphatase
D: RxLR effector protein PexRD24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2856
Polymers44,0512
Non-polymers2344
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-21 kcal/mol
Surface area16320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.492, 57.036, 59.015
Angle α, β, γ (deg.)84.35, 86.49, 89.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Serine/threonine-protein phosphatase


Mass: 33600.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: 102587690 / Production host: Escherichia coli (E. coli) / References: UniProt: M1C5B8
#2: Protein RxLR effector protein PexRD24


Mass: 10450.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans (potato late blight agent)
Gene: PexRD24, PITG_04314 / Production host: Escherichia coli (E. coli) / References: UniProt: D0N0Z8
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.11 Å3/Da / Density % sol: 41.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium fluoride, 0.1 M BIS-TRIS propose pH 8.5, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91188 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 2.1→58.62 Å / Num. obs: 40927 / % possible obs: 97.6 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rrim(I) all: 0.097 / Net I/σ(I): 9.2
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3300 / CC1/2: 0.84 / Rrim(I) all: 0.527

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INB

5inb


Resolution: 2.1→58.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.158 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25141 1979 4.8 %RANDOM
Rwork0.20246 ---
obs0.20482 38877 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.062 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å2-0.24 Å20.74 Å2
2---0.82 Å2-1.22 Å2
3---3.12 Å2
Refinement stepCycle: 1 / Resolution: 2.1→58.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5889 0 16 211 6116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165800
X-RAY DIFFRACTIONr_angle_refined_deg1.6591.6528118
X-RAY DIFFRACTIONr_angle_other_deg0.5471.5813368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.926534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.565101097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2882
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026996
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021400
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5052.2822916
X-RAY DIFFRACTIONr_mcbond_other2.5012.2822916
X-RAY DIFFRACTIONr_mcangle_it4.1074.083638
X-RAY DIFFRACTIONr_mcangle_other4.1074.0823639
X-RAY DIFFRACTIONr_scbond_it2.6692.5123108
X-RAY DIFFRACTIONr_scbond_other2.6682.5143109
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2664.5044481
X-RAY DIFFRACTIONr_long_range_B_refined7.34523.066981
X-RAY DIFFRACTIONr_long_range_B_other7.36323.056949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 134 -
Rwork0.268 2843 -
obs--96.28 %
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)
12.49950.9468-0.11133.1511-0.43171.91160.0168-0.3052-0.28850.2725-0.08460.22330.281-0.18440.06780.0804-0.03240.04720.05790.02830.078422.2242-32.54051.1786
22.2554-0.31221.18941.6058-1.34865.103-0.01780.36760.1503-0.1766-0.0388-0.0183-0.20270.19110.05660.0597-0.00750.01790.0860.00820.049724.7637-12.9245-20.2894
32.2535-0.98260.11472.5265-0.44292.16980.03620.26680.2436-0.2574-0.09310.0738-0.4488-0.14290.05690.1460.0377-0.03540.04290.02510.0447-5.49064.4393-20.1893
42.07730.2732-1.23141.7459-0.85975.63360.0668-0.2099-0.10920.1531-0.0824-0.05130.19650.14960.01550.0453-0.0129-0.04110.02320.01650.0831-2.3941-14.84420.0545
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 295
2X-RAY DIFFRACTION2B68 - 143
3X-RAY DIFFRACTION3C7 - 295
4X-RAY DIFFRACTION4D69 - 145

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