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- PDB-9ktq: Crystal structure of the pathogen-secreted apoplastic GH12 xylogl... -

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Basic information

Entry
Database: PDB / ID: 9ktq
TitleCrystal structure of the pathogen-secreted apoplastic GH12 xyloglucan-specific endoglucanase XEG1
ComponentsXyloglucan-specific endo-beta-1,4-glucanase 1
KeywordsHYDROLASE / xyloglucanase / XEG / oomycetes / Phytophthora sojae
Function / homology
Function and homology information


symbiont-mediated disruption of host cell wall / xyloglucan-specific endo-beta-1,4-glucanase / xyloglucan-specific endo-beta-1,4-glucanase activity / host cellular component / cellulase activity / polysaccharide catabolic process / extracellular region
Similarity search - Function
Glycoside hydrolase family 12 / Glycosyl hydrolase family 12 / Glycoside hydrolase family 11/12 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Xyloglucan-specific endo-beta-1,4-glucanase 1
Similarity search - Component
Biological speciesPhytophthora sojae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsXia, Y.Q. / Liu, L. / Zhang, Q. / Shi, X.C. / Wang, Z.K. / Zhang, Z.C. / He, X.Y. / Xiao, J.H. / Jiang, H.B. / Zhang, S.C. ...Xia, Y.Q. / Liu, L. / Zhang, Q. / Shi, X.C. / Wang, Z.K. / Zhang, Z.C. / He, X.Y. / Xiao, J.H. / Jiang, H.B. / Zhang, S.C. / Yang, Y.H. / Ye, W.W. / Wang, Z.Y. / Wang, Y. / Ma, Z.C. / Yang, Q. / Wang, Y.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31721004 China
CitationJournal: To Be Published
Title: A nature product XSMl directly targets xyloglucanases to inhibit filamentous pathogen infection
Authors: Xia, Y.Q. / Liu, L. / Zhang, Q. / Shi, X.C. / Wang, Z.K. / Zhang, Z.C. / He, X.Y. / Xiao, J.H. / Jiang, H.B. / Zhang, S.C. / Yang, Y.H. / Ye, W.W. / Wang, Z.Y. / Wang, Y. / Ma, Z.C. / Yang, Q. / Wang, Y.C.
History
DepositionDec 2, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xyloglucan-specific endo-beta-1,4-glucanase 1


Theoretical massNumber of molelcules
Total (without water)25,7701
Polymers25,7701
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization, Panta
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.283, 140.283, 140.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Xyloglucan-specific endo-beta-1,4-glucanase 1 / Glycoside hydrolase family 12 protein XEG1 / GH12 protein XEG1


Mass: 25769.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora sojae (strain P6497) (eukaryote)
Gene: XEG1, PHYSODRAFT_559651 / Production host: Komagataella pastoris (fungus)
References: UniProt: G4ZHR2, xyloglucan-specific endo-beta-1,4-glucanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 4.83 Å3/Da / Density % sol: 74.53 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 5% v/v TacsimateTM pH 7.0, 0.1 M HEPES pH 7.0, 10% w/v Polyethylene glycol monomethyl ether 5,000

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Data collection

DiffractionMean temperature: 273 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Nov 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.07→49.6 Å / Num. obs: 28081 / % possible obs: 99.98 % / Redundancy: 20 % / Biso Wilson estimate: 19.38 Å2 / CC1/2: 0.992 / Net I/σ(I): 10.3
Reflection shellResolution: 2.071→2.145 Å / Rmerge(I) obs: 0.579 / Num. unique obs: 2759

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7W3V

7w3v


Resolution: 2.07→49.6 Å / SU ML: 0.219 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.2259
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2104 1999 7.12 %
Rwork0.1904 26082 -
obs0.1919 28081 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.13 Å2
Refinement stepCycle: LAST / Resolution: 2.07→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 0 342 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461774
X-RAY DIFFRACTIONf_angle_d0.67762412
X-RAY DIFFRACTIONf_chiral_restr0.0501272
X-RAY DIFFRACTIONf_plane_restr0.0044298
X-RAY DIFFRACTIONf_dihedral_angle_d13.0471607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.120.3041460.28621869X-RAY DIFFRACTION99.9
2.12-2.180.27651410.25741848X-RAY DIFFRACTION100
2.18-2.240.23751360.23751826X-RAY DIFFRACTION100
2.24-2.320.27481430.23971847X-RAY DIFFRACTION100
2.32-2.40.26031390.21891848X-RAY DIFFRACTION100
2.4-2.490.23941420.20421848X-RAY DIFFRACTION100
2.5-2.610.21631420.19661863X-RAY DIFFRACTION100
2.61-2.750.25941440.20281857X-RAY DIFFRACTION100
2.75-2.920.23221400.19411844X-RAY DIFFRACTION100
2.92-3.140.20811470.18321861X-RAY DIFFRACTION100
3.14-3.460.17231420.16871865X-RAY DIFFRACTION100
3.46-3.960.14871470.14781864X-RAY DIFFRACTION100
3.96-4.980.16031490.13271885X-RAY DIFFRACTION100
4.99-100.21631410.19911957X-RAY DIFFRACTION99.9

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