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- PDB-8ebb: Crystal structure of SIX6 from Fusarium oxysporum f. sp. lycopersici -

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Basic information

Entry
Database: PDB / ID: 8ebb
TitleCrystal structure of SIX6 from Fusarium oxysporum f. sp. lycopersici
Components(Secreted in xylem Six6) x 2
KeywordsUNKNOWN FUNCTION / Fungal effector / SIX6
Function / homologyD(-)-TARTARIC ACID / Secreted in xylem Six6
Function and homology information
Biological speciesFusarium oxysporum f. sp. lycopersici (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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
Revision 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: Secreted in xylem Six6
B: Secreted in xylem Six6
C: Secreted in xylem Six6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2905
Polymers42,9903
Non-polymers3002
Water3,441191
1
A: Secreted in xylem Six6
C: Secreted in xylem Six6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2783
Polymers24,1282
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area9540 Å2
MethodPISA
2
B: Secreted in xylem Six6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0122
Polymers18,8621
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint1 kcal/mol
Surface area10030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.303, 93.544, 60.489
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Secreted in xylem Six6


Mass: 18862.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: SIX6 protein with pro-domain removed
Source: (gene. exp.) Fusarium oxysporum f. sp. lycopersici (fungus)
Gene: SIX6 / Production host: Escherichia coli (E. coli) / References: UniProt: C9WMG8
#2: Protein/peptide Secreted in xylem Six6


Mass: 5265.721 Da / Num. of mol.: 1 / Fragment: prodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium oxysporum f. sp. lycopersici (fungus)
Gene: SIX6 / Production host: Escherichia coli (E. coli) / References: UniProt: C9WMG8
#3: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Ammonium tartrate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95336 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95336 Å / Relative weight: 1
ReflectionResolution: 1.88→47.4 Å / Num. obs: 35252 / % possible obs: 96.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.81 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Rrim(I) all: 0.082 / Net I/σ(I): 11.8
Reflection shellResolution: 1.88→1.92 Å / Rmerge(I) obs: 1.429 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2205 / CC1/2: 0.571 / Rpim(I) all: 0.857 / Rrim(I) all: 1.668

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SIX6 alphafold model

Resolution: 1.88→46.77 Å / SU ML: 0.2254 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.3959
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 2000 5.68 %
Rwork0.1932 33206 -
obs0.1948 35206 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.73 Å2
Refinement stepCycle: LAST / Resolution: 1.88→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2787 0 20 191 2998
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822873
X-RAY DIFFRACTIONf_angle_d0.93263897
X-RAY DIFFRACTIONf_chiral_restr0.0623414
X-RAY DIFFRACTIONf_plane_restr0.0092513
X-RAY DIFFRACTIONf_dihedral_angle_d5.98389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.920.3111390.28512310X-RAY DIFFRACTION96.61
1.92-1.980.28851400.25632317X-RAY DIFFRACTION97.46
1.98-2.030.27431420.25142356X-RAY DIFFRACTION97.16
2.03-2.10.28391390.24012316X-RAY DIFFRACTION97.19
2.1-2.170.30751420.21882367X-RAY DIFFRACTION97.63
2.17-2.260.28891410.21982329X-RAY DIFFRACTION97.74
2.26-2.360.2351370.22072266X-RAY DIFFRACTION94.35
2.36-2.490.30391440.2312389X-RAY DIFFRACTION98.37
2.49-2.650.28291430.23312377X-RAY DIFFRACTION97.83
2.65-2.850.241450.20552406X-RAY DIFFRACTION98.99
2.85-3.140.2071440.20952398X-RAY DIFFRACTION98.57
3.14-3.590.21871450.18672422X-RAY DIFFRACTION98.35
3.59-4.520.17741420.15352355X-RAY DIFFRACTION95.02
4.52-46.770.16561570.15992598X-RAY DIFFRACTION99.21
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)
13.24396796987-2.65885683429-0.01887797124867.459941798170.4528462782881.51141478844-0.0996776725616-0.08478681055470.09132543006590.3919650580670.267528406617-0.647036212915-0.09396665527820.0318426214861-0.2074227748170.256188025144-0.00248474756028-0.06641617851580.224032795169-0.01695156244780.27664373462911.67572937398.57865073355.71548544818
24.094577965410.541530509916-0.987558699323.33757296692-0.2230056821972.14407680556-0.09605336936030.07916438341740.09952033474310.1121903124880.1188053204680.191718664236-0.100099059832-0.104698788845-0.02641438445790.2274143271320.0272858584477-0.0109803164660.1920697008960.005627392446320.209325098368-2.6050767806223.82686153090.221310568547
35.10535478103-0.9414471493443.091225226551.15566364547-0.3308008794531.96954989332-0.06715251549310.0613051028003-0.523025115780.09728099597490.3421508545750.288147351657-0.320401888915-0.154433801437-0.3031022362220.3698262184550.00452910657310.01419682253030.4054619762760.08977622408320.360569756813-14.2456957279.43898111438-28.8779871418
44.704661420882.60135201069-3.557646579283.60088105989-3.390327867193.63510267319-0.04778644454270.4602852309910.2829637606450.06116542603020.2413580009980.539363949398-0.7388450766110.436948239812-0.1123225256690.467065397046-0.179403761523-0.05579160769460.6381063616280.1883416339610.420794891569-11.53679528266.37794252932-31.1631870901
52.997139320061.25024167830.5559473134763.253577641381.172277795462.93802332332-0.1599468510440.4446718928230.0843367292645-0.1589594580730.334564105932-0.220346853146-0.1176373043850.0401971618272-0.168787277860.328244502967-0.06121038897280.04447075765670.3672993155090.02380285004780.2380560242177.5631610012121.353394823-24.6010655562
62.20388847709-1.484280072372.521006681223.492762602161.380877988039.75741147794-0.161679584816-0.08423238411240.8319376724790.533754015707-0.2190888577190.767363939732-0.820597785961-0.49695449710.278226985240.4258991342530.0745566148354-0.01830100351980.241523355336-0.07525091161130.545227139042-2.2544237839435.5424295165.58488419975
74.12564419198-4.83084773355-1.60984091485.722195828421.389945919414.599384020150.0721908466715-0.4791807836290.3021473193350.2816029718260.196514109539-0.785863844043-0.2348314865410.172321153933-0.2660208531250.449258883936-0.0523729813919-0.06250479143780.286980935722-0.03681231449460.39751417434610.160005190828.54959612045.21103629571
88.03207293835-7.57768585668-6.344149114577.577317972516.809063646266.59608750117-0.139313944395-0.531030599319-0.643132639487-0.2393825995240.80315770865-0.986128981450.3855538084550.963989671961-0.516225977980.2101983780470.0223233830343-0.01112852734440.309468416099-0.06079515606720.65873908692819.633368576517.78965831660.518649843332
90.8245532779070.981284311262-1.961971226725.65700741590.6380909798616.650182424530.511610540080.1955221987420.172435026779-0.9045153283650.296615205676-0.3395729900960.127326377863-0.211966918298-0.6168881319360.5348812945050.07916867402070.1231309155880.3933926060850.2022115283621.1027833763518.268774936814.8242979869-2.63169508435
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 58 through 127 )AA58 - 1271 - 70
22chain 'A' and (resid 128 through 226 )AA128 - 22671 - 169
33chain 'B' and (resid 57 through 88 )BC57 - 881 - 32
44chain 'B' and (resid 89 through 105 )BC89 - 10533 - 49
55chain 'B' and (resid 106 through 226 )BC106 - 22650 - 170
66chain 'C' and (resid 29 through 33 )CE29 - 331 - 5
77chain 'C' and (resid 34 through 38 )CE34 - 386 - 10
88chain 'C' and (resid 39 through 43 )CE39 - 4311 - 15
99chain 'C' and (resid 44 through 46 )CE44 - 4616 - 18

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