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- PDB-8eb9: Crystal structure of SIX8 from Fusarium oxysporum f. sp. lycopersici -

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Entry
Database: PDB / ID: 8eb9
TitleCrystal structure of SIX8 from Fusarium oxysporum f. sp. lycopersici
ComponentsSecreted in xylem Six8
KeywordsUNKNOWN FUNCTION / Fungal effector / SIX8
Function / homologySecreted in xylem Six8
Function and homology information
Biological speciesFusarium oxysporum f. sp. lycopersici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsYu, D.S. / Ericsson, D.J. / Williams, S.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP200100388 Australia
Australian Research Council (ARC)FT200100135 Australia
Citation
Journal: Elife / Year: 2024
Title: The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies.
Authors: Yu, D.S. / Outram, M.A. / Smith, A. / McCombe, C.L. / Khambalkar, P.B. / Rima, S.A. / Sun, X. / Ma, L. / Ericsson, D.J. / Jones, D.A. / Williams, S.J.
#1: Journal: Elife / Year: 2023
Title: The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies
Authors: Yu, D.S. / Outram, M.A. / Smith, A. / McCombe, C.L. / Khambalkar, P.B. / Rima, S.A. / Sun, X. / Ma, L. / Ericsson, D.J. / Jones, D.A. / Williams, S.J.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#3: Journal: J Synchrotron Radiat / Year: 2015
Title: MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron.
Authors: Cowieson, N.P. / Aragao, D. / Clift, M. / Ericsson, D.J. / Gee, C. / Harrop, S.J. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi-Tunnicliffe, A. / Williamson, R. / Caradoc-Davies, T.
#4: Journal: J Synchrotron Radiat / Year: 2018
Title: MX2: a high-flux undulator microfocus beamline serving both the chemical and macromolecular crystallography communities at the Australian Synchrotron.
Authors: Aragao, D. / Aishima, J. / Cherukuvada, H. / Clarken, R. / Clift, M. / Cowieson, N.P. / Ericsson, D.J. / Gee, C.L. / Macedo, S. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi- ...Authors: Aragao, D. / Aishima, J. / Cherukuvada, H. / Clarken, R. / Clift, M. / Cowieson, N.P. / Ericsson, D.J. / Gee, C.L. / Macedo, S. / Mudie, N. / Panjikar, S. / Price, J.R. / Riboldi-Tunnicliffe, A. / Rostan, R. / Williamson, R. / Caradoc-Davies, T.T.
History
DepositionAug 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.citation_id
Revision 1.2Mar 13, 2024Group: Database references / Category: citation / citation_author
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Secreted in xylem Six8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0572
Polymers9,9611
Non-polymers961
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.814, 51.814, 81.599
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Components on special symmetry positions
IDModelComponents
11A-263-

HOH

21A-270-

HOH

31A-284-

HOH

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Components

#1: Protein Secreted in xylem Six8


Mass: 9961.280 Da / Num. of mol.: 1 / Mutation: C58S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum f. sp. lycopersici (fungus)
Gene: SIX8 / Production host: Escherichia coli (E. coli) / References: UniProt: C9WMH0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.17 M Ammonium sulfate, 15% glycerol, 25.5% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.28→36.64 Å / Num. obs: 29449 / % possible obs: 99.98 % / Redundancy: 13 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04763 / Rpim(I) all: 0.01399 / Rrim(I) all: 0.04971 / Net I/σ(I): 23.71
Reflection shellResolution: 1.28→1.326 Å / Rmerge(I) obs: 1.35 / Num. unique obs: 2869 / CC1/2: 0.725 / Rrim(I) all: 1.405 / Rsym value: 0.3879 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SIX8 alphafold model

Resolution: 1.28→36.64 Å / SU ML: 0.1305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6706
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1933 2000 6.79 %
Rwork0.17 27449 -
obs0.1715 29449 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.79 Å2
Refinement stepCycle: LAST / Resolution: 1.28→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms653 0 5 84 742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0108665
X-RAY DIFFRACTIONf_angle_d1.2101903
X-RAY DIFFRACTIONf_chiral_restr0.1009111
X-RAY DIFFRACTIONf_plane_restr0.0208115
X-RAY DIFFRACTIONf_dihedral_angle_d6.172896
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.31021390.26571902X-RAY DIFFRACTION98.79
1.31-1.350.30181390.2151909X-RAY DIFFRACTION99.95
1.35-1.390.23061400.1931929X-RAY DIFFRACTION100
1.39-1.430.19631410.17141935X-RAY DIFFRACTION100
1.43-1.480.17721410.16241930X-RAY DIFFRACTION100
1.48-1.540.20231410.16271929X-RAY DIFFRACTION100
1.54-1.610.17361410.15451949X-RAY DIFFRACTION100
1.61-1.70.18721410.13911924X-RAY DIFFRACTION99.95
1.7-1.80.16451420.14011956X-RAY DIFFRACTION100
1.8-1.940.15561440.14431963X-RAY DIFFRACTION100
1.94-2.140.19121420.14421961X-RAY DIFFRACTION100
2.14-2.450.17331460.15341999X-RAY DIFFRACTION100
2.45-3.080.18291460.1822013X-RAY DIFFRACTION100
3.08-36.640.21121570.18522150X-RAY DIFFRACTION99.91

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