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- PDB-6wes: Crystal structure of the effector SnTox3 from Parastagonospora nodorum -

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Basic information

Entry
Database: PDB / ID: 6wes
TitleCrystal structure of the effector SnTox3 from Parastagonospora nodorum
ComponentsTox3
KeywordsTOXIN / Fungal effector / beta barrel / disulfide bond
Function / homologyTox3
Function and homology information
Biological speciesPhaeosphaeria nodorum
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.36 Å
AuthorsOutram, M.A. / Williams, S.J. / Ericsson, D.J. / Kobe, B. / Solomon, P.S.
Funding support Australia, 6items
OrganizationGrant numberCountry
Australian Research Council (ARC)DE160100893 Australia
Australian Research Council (ARC)DP160102244 Australia
Australian Research Council (ARC)DP190102526 Australia
Australian Research Council (ARC)DP180102355 Australia
Australian Research Council (ARC)DP120103558 Australia
Australian Research Council (ARC)FL180100109 Australia
Citation
Journal: New Phytol. / Year: 2021
Title: The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease ...Title: The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and provides insight into Snn3 recognition and pro-domain protease processing of fungal effectors.
Authors: Outram, M.A. / Sung, Y.C. / Yu, D. / Dagvadorj, B. / Rima, S.A. / Jones, D.A. / Ericsson, D.J. / Sperschneider, J. / Solomon, P.S. / Kobe, B. / Williams, S.J.
#1: Journal: Biorxiv / Year: 2021
Title: The crystal structure of SnTox3 from the necrotrophic fungus Parastagonospora nodorum reveals a unique effector fold and insights into Kex2 protease processing of fungal effectors
Authors: Outram, M.A. / Sung, Y.C. / Yu, D. / Dagvadorj, B. / Rima, S. / Jones, D.A. / Ericsson, D.J. / Sperschneider, J. / Solomon, P.S. / Kobe, B. / Williams, S.J.
History
DepositionApr 2, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / citation_author
Revision 1.3Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tox3


Theoretical massNumber of molelcules
Total (without water)17,8961
Polymers17,8961
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Identified via SEC-MALS to be predominantly a monomer in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.870, 29.910, 56.050
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Tox3


Mass: 17896.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeosphaeria nodorum (strain SN15 / ATCC MYA-4574 / FGSC 10173) (fungus)
Strain: SN15 / ATCC MYA-4574 / FGSC 10173 / Gene: Tox3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C5IAW5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M Tris pH 7.6, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.359→26.02 Å / Num. obs: 34893 / % possible obs: 98.71 % / Redundancy: 3 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02734 / Rrim(I) all: 0.03326 / Net I/σ(I): 22.31
Reflection shellResolution: 1.359→1.407 Å / Redundancy: 3 % / Rmerge(I) obs: 0.3028 / Mean I/σ(I) obs: 3.79 / Num. unique obs: 3364 / CC1/2: 0.9 / CC star: 0.973 / Rrim(I) all: 0.3704 / % possible all: 95.79

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSVERSION Nov 1, 2016data reduction
XSCALEVERSION Nov 1, 2016data scaling
CRANK2phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: SAD / Resolution: 1.36→26.02 Å / SU ML: 0.1172 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.9063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1989 1944 5.57 %
Rwork0.1735 32947 -
obs0.1748 34891 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.71 Å2
Refinement stepCycle: LAST / Resolution: 1.36→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1253 0 0 157 1410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00961284
X-RAY DIFFRACTIONf_angle_d1.05431753
X-RAY DIFFRACTIONf_chiral_restr0.0989196
X-RAY DIFFRACTIONf_plane_restr0.0068236
X-RAY DIFFRACTIONf_dihedral_angle_d14.7899177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.24911310.23292218X-RAY DIFFRACTION94.19
1.39-1.430.22451390.23212359X-RAY DIFFRACTION99.84
1.43-1.470.25291390.21182350X-RAY DIFFRACTION99.8
1.47-1.520.25631400.20132375X-RAY DIFFRACTION99.72
1.52-1.570.21811410.19322369X-RAY DIFFRACTION99.72
1.57-1.640.22991380.18372354X-RAY DIFFRACTION99.8
1.64-1.710.2011390.18132362X-RAY DIFFRACTION99.88
1.71-1.80.20891390.18012349X-RAY DIFFRACTION99.72
1.8-1.910.19641410.17612368X-RAY DIFFRACTION99.68
1.91-2.060.19371390.15832367X-RAY DIFFRACTION99.6
2.06-2.270.18981410.1712392X-RAY DIFFRACTION99.53
2.27-2.60.2071410.18132374X-RAY DIFFRACTION99.37
2.6-3.270.19291400.17262387X-RAY DIFFRACTION98.44
3.27-26.020.17371360.1512323X-RAY DIFFRACTION93.29
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.06641971152120.08458533783730.05814453290210.105643682798-0.02497953417160.0299385192886-0.05358264834710.0295217665132-0.000344000996987-0.1973422236590.06214544822570.01207221801970.0241789576178-0.0426737482941-0.004142680810010.112512047392-0.01018526272450.001961484084230.08684706955050.008756754873480.133243984041-18.4496006259-2.1787599047319.4835819323
20.275595551439-0.108038351897-0.06900264350290.5345993117690.2417245574990.46035929056-0.0273895177280.005574620868460.0285892884675-0.3119120590280.019872714628-0.01215776961340.0106492706716-0.003278308023180.002752187579490.123265272294-0.002108331895630.01016272171480.09152076176450.006222972723830.0960049379653-7.79417179454.1280872511412.7884840803
30.0577196751964-0.01947592934220.0009912469032940.0649769324522-0.01250211388340.0164370326858-0.0301536512626-0.197641860144-0.1705547543540.166712701855-0.003995233916140.04541139651730.06620087884970.141032718941-7.75503017727E-50.107388166416-0.0171302187270.0008888796233770.1235442710810.008104550888170.114727046478-25.4196381767-15.905594089534.0998383535
40.207996206996-0.005714436252820.006226713105010.6676058488210.1392451172140.150796736513-0.0246685846629-0.0359849432967-0.000461708084948-0.02399623744860.06298863873740.02360079462250.03010380937860.006901213298340.007352750177130.0950680934597-0.00811652455958-0.01130057632260.0970506713568-0.003809607235510.0902113486768-11.9207908488-9.1142916801223.344566254
50.35590879304-0.06627060750970.1635202108490.00657251453412-0.09741909994790.115811251006-0.02256560848510.04563140861040.0778539420067-0.05405276136350.03752805032950.04305706358510.0763703300950.141288876806-0.0267302629130.129355354779-0.02156081701260.01038785053770.127116334805-0.0051335681430.0859699876546-3.762179199360.049085043580113.8539475544
60.1217542744520.1160902826270.1096894087890.04172624216790.05222384856250.1324950674170.00836475698959-0.0509351991954-0.0167933899842-0.0256025586537-0.01177726507110.0222942312821-0.05195478552440.0932775283478-0.007060968420540.1152872276240.01042553099650.003120370299010.09627570096190.002283066852420.0922098614792-5.597977483351.7408281113516.2249184435
70.1454812319190.04884067585440.09230263249850.1523574414120.1704457680380.72075419990.148013966633-0.103251803410.07847916443010.0305131850475-0.07960183752690.076291364638-0.104031976780.1189142005190.0157610208540.08989320634920.03151664827910.01057204821270.08692252091220.005787910710670.112878463015-11.58100879021.463204988822.4530558073
80.8247390748390.18981062293-0.1457687285310.265277859218-0.1540828475230.0810709815911-0.1360836610120.04657419203240.07378498435020.1474993284020.105346901052-0.03772011987830.3922000382620.3486710017240.06042594763920.2563909757260.0727118315842-0.008153889516520.251072001124-0.04084785983040.09108397441478.528210499651.1589985913910.0132811869
90.0558806652173-0.0947995347876-0.0747785551880.1728546062660.03358292896410.203697036909-0.0009817419309430.03406541946680.0738407065261-0.1210954424750.0386286851974-0.00275712872101-0.137045972968-0.1457498383110.001095554636790.1029257177340.00901961560773-0.006760027102620.114385522646-0.006936994453520.105425431496-13.843905313910.495668213815.3220276701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 33 )
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 44 )
4X-RAY DIFFRACTION4chain 'A' and (resid 45 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 110 )
7X-RAY DIFFRACTION7chain 'A' and (resid 111 through 133 )
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 158 )

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