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- PDB-7b76: Crystal structure of the effector AvrLm5-9 from Leptosphaeria maculans -

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Basic information

Entry
Database: PDB / ID: 7b76
TitleCrystal structure of the effector AvrLm5-9 from Leptosphaeria maculans
ComponentsAvirulence protein LmJ1
KeywordsSIGNALING PROTEIN / AVIRULENCE PROTEIN / AVIRULENCE EFFECTOR PROTEIN / FUNGAL PROTEIN / Fulvia fulva
Function / homologyIODIDE ION / Avirulence protein LmJ1
Function and homology information
Biological speciesLeptosphaeria maculans (blackleg of rapeseed fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLazar, N. / Mesarich, C. / Petit-Houdenot, Y. / Talbi, N. / Li de la Sierra-Gallay, I. / Zelie, E. / Blondeau, K. / Gracy, J. / Ollivier, B. / van de Wouw, A. ...Lazar, N. / Mesarich, C. / Petit-Houdenot, Y. / Talbi, N. / Li de la Sierra-Gallay, I. / Zelie, E. / Blondeau, K. / Gracy, J. / Ollivier, B. / van de Wouw, A. / Balesdent, M.H. / Idnurm, A. / van Tilbeurgh, H. / Fudal, I.
Funding support France, 5items
OrganizationGrant numberCountry
French National Research AgencyANR-14-CE19-0019 France
French National Research AgencyANR-17-EUR-0007 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-05 France
Centre National de la Recherche Scientifique (CNRS) France
French National Research AgencyANR-13-BS07-0007-01 to EG France
Citation
Journal: Plos Pathog. / Year: 2022
Title: A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins.
Authors: Lazar, N. / Mesarich, C.H. / Petit-Houdenot, Y. / Talbi, N. / Li de la Sierra-Gallay, I. / Zelie, E. / Blondeau, K. / Gracy, J. / Ollivier, B. / Blaise, F. / Rouxel, T. / Balesdent, M.H. / ...Authors: Lazar, N. / Mesarich, C.H. / Petit-Houdenot, Y. / Talbi, N. / Li de la Sierra-Gallay, I. / Zelie, E. / Blondeau, K. / Gracy, J. / Ollivier, B. / Blaise, F. / Rouxel, T. / Balesdent, M.H. / Idnurm, A. / van Tilbeurgh, H. / Fudal, I.
#1: Journal: Plant J. / Year: 2015
Title: Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins.
Authors: Blondeau, K. / Blaise, F. / Graille, M. / Kale, S.D. / Linglin, J. / Ollivier, B. / Labarde, A. / Lazar, N. / Daverdin, G. / Balesdent, M.H. / Choi, D.H. / Tyler, B.M. / Rouxel, T. / van ...Authors: Blondeau, K. / Blaise, F. / Graille, M. / Kale, S.D. / Linglin, J. / Ollivier, B. / Labarde, A. / Lazar, N. / Daverdin, G. / Balesdent, M.H. / Choi, D.H. / Tyler, B.M. / Rouxel, T. / van Tilbeurgh, H. / Fudal, I.
History
DepositionDec 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Mar 1, 2023Group: Advisory / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Avirulence protein LmJ1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7484
Polymers14,3671
Non-polymers3813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area370 Å2
ΔGint-0 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 57.900, 212.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Avirulence protein LmJ1


Mass: 14367.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptosphaeria maculans (blackleg of rapeseed fungus)
Gene: AvrLmJ1, Lema_uP070880.2 / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: V5TFR9
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
Has ligand of interestN
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: 3.58 Å3/Da / Density % sol: 65.68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.7M sodium acetate, 80 mM nickel sulfate, 0.1 M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.4878 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4878 Å / Relative weight: 1
ReflectionResolution: 2.7→48.81 Å / Num. obs: 6425 / % possible obs: 99.8 % / Redundancy: 11.2 % / CC1/2: 0.992 / Rrim(I) all: 0.299 / Net I/σ(I): 8.75
Reflection shellResolution: 2.7→2.86 Å / Num. unique obs: 997 / CC1/2: 0.654 / Rrim(I) all: 2.22

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→48.81 Å / Cor.coef. Fo:Fc: 0.86 / Cor.coef. Fo:Fc free: 0.818 / SU B: 13.223 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3116 322 5 %RANDOM
Rwork0.2764 ---
obs0.2781 6425 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.22 Å2 / Biso mean: 42.727 Å2 / Biso min: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.33 Å20 Å2
2--0.67 Å20 Å2
3----2.17 Å2
Refinement stepCycle: final / Resolution: 2.7→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 3 0 979
Biso mean--80.81 --
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131003
X-RAY DIFFRACTIONr_bond_other_d0.0010.017878
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.6351360
X-RAY DIFFRACTIONr_angle_other_deg1.3051.582049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6915121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.78123.05159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.95215172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.373157
X-RAY DIFFRACTIONr_chiral_restr0.0690.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021118
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02199
LS refinement shellResolution: 2.7→2.768 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.388 23 -
Rwork0.456 434 -
obs--98.49 %

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