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- PDB-5od4: Avr2 effector protein from the fungal plant pathogen Fusarium oxy... -

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Basic information

Entry
Database: PDB / ID: 5od4
TitleAvr2 effector protein from the fungal plant pathogen Fusarium oxysporum
ComponentsSecreted in xylem 3
KeywordsUNKNOWN FUNCTION / effector / protein-protein interaction / beta-sandwich
Function / homologySecreted in xylem 3Secreted in xylem 3 protein / Secreted in the xylem 3
Function and homology information
Biological speciesFusarium oxysporum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsHughes, R.K. / Banfield, M.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilJ004553 United Kingdom
CitationJournal: New Phytol. / Year: 2017
Title: Structure-function analysis of the Fusarium oxysporum Avr2 effector allows uncoupling of its immune-suppressing activity from recognition.
Authors: Di, X. / Cao, L. / Hughes, R.K. / Tintor, N. / Banfield, M.J. / Takken, F.L.W.
History
DepositionJul 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2Oct 25, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature
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 in xylem 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3806
Polymers14,0701
Non-polymers3105
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint10 kcal/mol
Surface area7760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.410, 51.730, 74.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Secreted in xylem 3 / Secreted in xylem 3 protein / Avr2


Mass: 14069.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum (fungus) / Gene: SIX3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SHuffle / References: UniProt: Q2A0P1, UniProt: A0A0C4DI32*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES, pH 6.5; 25% (w/v) PEG 8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9168 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9168 Å / Relative weight: 1
ReflectionResolution: 1.1→42.54 Å / Num. obs: 53312 / % possible obs: 99.8 % / Redundancy: 12.8 % / Net I/σ(I): 26.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→40 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.603 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.027 / ESU R Free: 0.029 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16899 2672 5 %RANDOM
Rwork0.13876 ---
obs0.14026 50569 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.746 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--0.4 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 1.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 20 151 1137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191084
X-RAY DIFFRACTIONr_bond_other_d0.0030.02977
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9621486
X-RAY DIFFRACTIONr_angle_other_deg1.19432266
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4365143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.80120.78451
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30915154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5191515
X-RAY DIFFRACTIONr_chiral_restr0.110.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211218
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02245
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_it1.2050.97519
X-RAY DIFFRACTIONr_mcbond_other1.1730.967518
X-RAY DIFFRACTIONr_mcangle_it1.5111.466649
X-RAY DIFFRACTIONr_mcangle_other1.511.468650
X-RAY DIFFRACTIONr_scbond_it2.071.289565
X-RAY DIFFRACTIONr_scbond_other2.0491.289565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.4581.826827
X-RAY DIFFRACTIONr_long_range_B_refined3.28113.6831177
X-RAY DIFFRACTIONr_long_range_B_other3.00312.7981137
X-RAY DIFFRACTIONr_rigid_bond_restr2.23332061
X-RAY DIFFRACTIONr_sphericity_free22.702585
X-RAY DIFFRACTIONr_sphericity_bonded10.84252094
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.152 168 -
Rwork0.137 3565 -
obs--96.63 %

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