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- PDB-6gu1: SFI3 effector protein from the oomycete plant pathogen Phytophtho... -

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Basic information

Entry
Database: PDB / ID: 6gu1
TitleSFI3 effector protein from the oomycete plant pathogen Phytophthora infestans
ComponentsSecreted RxLR effector peptide protein, putative
KeywordsUNKNOWN FUNCTION / Effector protein
Function / homologyhost cell nucleolus / extracellular region / RxLR effector protein SFI3
Function and homology information
Biological speciesPhytophthora infestans (potato late blight agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHughes, R.K. / Banfield, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: New Phytol. / Year: 2019
Title: Phytophthora infestans effector SFI3 targets potato UBK to suppress early immune transcriptional responses.
Authors: He, Q. / McLellan, H. / Hughes, R.K. / Boevink, P.C. / Armstrong, M. / Lu, Y. / Banfield, M.J. / Tian, Z. / Birch, P.R.J.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted RxLR effector peptide protein, putative
B: Secreted RxLR effector peptide protein, putative


Theoretical massNumber of molelcules
Total (without water)22,5222
Polymers22,5222
Non-polymers00
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-33 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.080, 44.390, 62.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Secreted RxLR effector peptide protein, putative


Mass: 11260.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora infestans (strain T30-4) (eukaryote)
Strain: T30-4 / Gene: PITG_06087 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0N6D2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / 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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris Propane pH 7.5, 0.2 M sodium acetate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.7→36 Å / Num. obs: 13594 / % possible obs: 99.5 % / Redundancy: 9.4 % / Net I/σ(I): 22
Reflection shellResolution: 1.7→1.79 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 1.7→62.05 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.543 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27431 673 5 %RANDOM
Rwork0.21839 ---
obs0.22108 12897 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.788 Å2
Baniso -1Baniso -2Baniso -3
1-3.64 Å20 Å20 Å2
2---1.42 Å20 Å2
3----2.22 Å2
Refinement stepCycle: 1 / Resolution: 1.7→62.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 0 98 1014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02983
X-RAY DIFFRACTIONr_bond_other_d0.0010.02930
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9341340
X-RAY DIFFRACTIONr_angle_other_deg0.94232153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0125124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.15922.88945
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06415182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.035157
X-RAY DIFFRACTIONr_chiral_restr0.0940.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021079
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02224
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_it2.5933.033454
X-RAY DIFFRACTIONr_mcbond_other2.5843.026453
X-RAY DIFFRACTIONr_mcangle_it3.6524.505568
X-RAY DIFFRACTIONr_mcangle_other3.6544.515569
X-RAY DIFFRACTIONr_scbond_it3.1963.521529
X-RAY DIFFRACTIONr_scbond_other3.1933.531530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1125.06765
X-RAY DIFFRACTIONr_long_range_B_refined6.67935.6141264
X-RAY DIFFRACTIONr_long_range_B_other6.65235.0281235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 55 -
Rwork0.294 931 -
obs--99.9 %

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