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- PDB-6zus: Crystal structure of the effector Ecp11-1 from Fulvia fulva -

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Basic information

Entry
Database: PDB / ID: 6zus
TitleCrystal structure of the effector Ecp11-1 from Fulvia fulva
ComponentsExtracellular protein 11-1
KeywordsSIGNALING PROTEIN / AVIRULENCE PROTEIN / AVIRULENCE EFFECTOR PROTEIN / FUNGAL PROTEIN / Fulvia fulva
Function / homologymetal ion binding / DI(HYDROXYETHYL)ETHER / Ecp11-1
Function and homology information
Biological speciesPassalora fulva (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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
DepositionJul 23, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: 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: Extracellular protein 11-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,13410
Polymers16,3981
Non-polymers7369
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-117 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.640, 53.640, 86.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Extracellular protein 11-1


Mass: 16398.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Passalora fulva (fungus) / Gene: Ecp11-1 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A1P8YXI8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 2.93 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 21% PEG550MME, 10mM Zinc sulfate, 0.1 MES pH6.5, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9734 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9734 Å / Relative weight: 1
ReflectionResolution: 1.62→45.55 Å / Num. obs: 46421 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.998 / Rrim(I) all: 0.102 / Net I/σ(I): 10.56
Reflection shellResolution: 1.62→1.72 Å / Mean I/σ(I) obs: 0.86 / Num. unique obs: 7420 / CC1/2: 0.604 / Rrim(I) all: 0.142

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ZUQ

6zuq


Resolution: 1.62→45.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.798 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 750 3 %RANDOM
Rwork0.1842 ---
obs0.1848 7420 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.68 Å2 / Biso mean: 27.012 Å2 / Biso min: 15.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2--0.37 Å20 Å2
3----1.04 Å2
Refinement stepCycle: final / Resolution: 1.62→45.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1151 0 35 159 1345
Biso mean--60.36 38.98 -
Num. residues----143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121245
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181056
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.6411683
X-RAY DIFFRACTIONr_angle_other_deg1.4531.5892460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1155148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60322.29774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33315191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.912158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
LS refinement shellResolution: 1.62→1.659 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.486 1751 -
obs--97.55 %

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