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- PDB-9m65: Crystal structure of the pathogen-secreted apoplastic GH12 xylogl... -

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Basic information

Entry
Database: PDB / ID: 9m65
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 strain P6497 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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: Crystal structure of the pathogen-secreted apoplastic GH12 xyloglucan-specific endoglucanase XEG1
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
DepositionMar 7, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3402
Polymers25,7701
Non-polymers5711
Water77543
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)139.418, 139.418, 139.418
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: Chemical ChemComp-A1ENU / ~{N}-(4-ethoxyphenyl)-4-[(10~{R},15~{S})-10-(4-methylphenyl)-12,14-bis(oxidanylidene)-8,11,13-triazatetracyclo[7.7.0.0^{2,7}.0^{11,15}]hexadeca-1(9),2,4,6-tetraen-13-yl]benzamide


Mass: 570.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 4.38 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: SSRF / Beamline: BL02U1 / Wavelength: 0.97853 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Dec 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.59→49.29 Å / Num. obs: 14241 / % possible obs: 99.93 % / Redundancy: 20 % / Biso Wilson estimate: 46.4 Å2 / Rpim(I) all: 0.064 / Net I/σ(I): 15.9
Reflection shellResolution: 2.59→2.68 Å / Num. unique obs: 1414 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9KTQ

9ktq


Resolution: 2.59→49.29 Å / SU ML: 0.301 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.3576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2141 1421 9.98 %
Rwork0.1935 12817 -
obs0.1956 14238 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.37 Å2
Refinement stepCycle: LAST / Resolution: 2.59→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 43 43 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511823
X-RAY DIFFRACTIONf_angle_d0.79592482
X-RAY DIFFRACTIONf_chiral_restr0.049274
X-RAY DIFFRACTIONf_plane_restr0.003304
X-RAY DIFFRACTIONf_dihedral_angle_d16.0834613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.680.30841420.26511275X-RAY DIFFRACTION100
2.68-2.790.31881430.25381263X-RAY DIFFRACTION100
2.79-2.910.32681380.24891272X-RAY DIFFRACTION100
2.92-3.070.2781390.23591278X-RAY DIFFRACTION100
3.07-3.260.22831450.21871262X-RAY DIFFRACTION100
3.26-3.510.20241390.19581261X-RAY DIFFRACTION100
3.51-3.860.23141400.18061291X-RAY DIFFRACTION100
3.87-4.420.16941390.15281283X-RAY DIFFRACTION100
4.43-5.560.17211470.15441288X-RAY DIFFRACTION100
5.57-49.290.18691490.20231344X-RAY DIFFRACTION99.4

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