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- PDB-5l7s: Crystal structure of RXLR effector PexRD54 from Phytophthora infestans -

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Basic information

Entry
Database: PDB / ID: 5l7s
TitleCrystal structure of RXLR effector PexRD54 from Phytophthora infestans
ComponentsSecreted RxLR effector peptide protein
KeywordsSIGNALING PROTEIN / RXLR Effector / Phytophthora infestans
Function / homologyRXLR phytopathogen effector protein, WY-domain / RXLR phytopathogen effector protein WY-domain / : / Effector PexRD54, WY-domain / host cell cytoplasm / host cell nucleus / extracellular region / RxLR effector protein 54
Function and homology information
Biological speciesPhytophthora infestans (potato late blight agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsMaqbool, A. / Hughes, R.K. / Banfield, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilNGRB United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54.
Authors: Maqbool, A. / Hughes, R.K. / Dagdas, Y.F. / Tregidgo, N. / Zess, E. / Belhaj, K. / Round, A. / Bozkurt, T.O. / Kamoun, S. / Banfield, M.J.
History
DepositionJun 3, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Structure summary
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted RxLR effector peptide protein


Theoretical massNumber of molelcules
Total (without water)34,0691
Polymers34,0691
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.160, 89.160, 144.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Secreted RxLR effector peptide protein / PexRD54


Mass: 34068.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans (potato late blight agent)
Gene: PITG_09316 / Production host: Escherichia coli (E. coli) / References: UniProt: D0NBE6

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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: 4.86 Å3/Da / Density % sol: 74.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 18% PEG 10K, 0.1M sodium acetate pH 5.0, 0.18M tri-ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.9→77.21 Å / Num. obs: 14463 / % possible obs: 99.8 % / Observed criterion σ(F): 2.9 / Redundancy: 12.1 % / Rsym value: 0.07 / Net I/σ(I): 24.9
Reflection shellResolution: 2.9→2.98 Å / Rsym value: 1.349

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→77.21 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.25 / SU ML: 0.251 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.297 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25649 764 5 %RANDOM
Rwork0.23 ---
obs0.23126 14463 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 98.278 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å21.21 Å20 Å2
2--2.42 Å20 Å2
3----7.85 Å2
Refinement stepCycle: 1 / Resolution: 2.9→77.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 0 0 2224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192270
X-RAY DIFFRACTIONr_bond_other_d0.0010.022190
X-RAY DIFFRACTIONr_angle_refined_deg1.0471.9573058
X-RAY DIFFRACTIONr_angle_other_deg0.86435032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2585264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14424.138116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64515433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8081517
X-RAY DIFFRACTIONr_chiral_restr0.0550.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
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_it2.8079.6581065
X-RAY DIFFRACTIONr_mcbond_other2.7799.6561064
X-RAY DIFFRACTIONr_mcangle_it4.51314.481326
X-RAY DIFFRACTIONr_mcangle_other4.51214.4831327
X-RAY DIFFRACTIONr_scbond_it2.78110.0081205
X-RAY DIFFRACTIONr_scbond_other2.7810.0121206
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.81914.8591733
X-RAY DIFFRACTIONr_long_range_B_refined8.58690.7929235
X-RAY DIFFRACTIONr_long_range_B_other8.58690.7969236
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 58 -
Rwork0.405 1074 -
obs--99.74 %

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