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- PDB-9g18: Structure of PslG with an iminosugar inhibitor -

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Basic information

Entry
Database: PDB / ID: 9g18
TitleStructure of PslG with an iminosugar inhibitor
ComponentsPslG
KeywordsHYDROLASE / endo-beta-glucanase / iminosugar / complex
Function / homology: / polysaccharide biosynthetic process / single-species biofilm formation / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / PslG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOffen, W.A. / Davies, G.J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Bespoke Activity-Based Probes Reveal that the Pseudomonas aeruginosa Endoglycosidase, PslG, Is an Endo-beta-glucanase.
Authors: Ruijgrok, G. / Offen, W.A. / Pickles, I.B. / Raju, D. / Patsos, T. / de Boer, C. / Ofman, T. / Rompa, J. / van Oord, D. / Dodson, E.J. / Beekers, A. / Voskuilen, T. / Ferrari, M. / Wu, L. / ...Authors: Ruijgrok, G. / Offen, W.A. / Pickles, I.B. / Raju, D. / Patsos, T. / de Boer, C. / Ofman, T. / Rompa, J. / van Oord, D. / Dodson, E.J. / Beekers, A. / Voskuilen, T. / Ferrari, M. / Wu, L. / Janssen, A.P.A. / Codee, J.D.C. / Howell, P.L. / Davies, G.J. / Overkleeft, H.S.
History
DepositionJul 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PslG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,74310
Polymers47,3811
Non-polymers1,3639
Water11,277626
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-12 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.604, 97.604, 119.852
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

#1: Protein PslG


Mass: 47380.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: This sequence includes a thrombin-cleavable N-terminal hexahistidine tag, which is removed prior to crystallization
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pslG, PA2237 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I1N2
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-alpha-L- ...alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-1-DEOXYNOJIRIMYCIN


Type: oligosaccharide / Mass: 795.735 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,5,4/[h2122h_1-5*N*][a2211m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3-4/a3-b1_b3-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][<C6N1O3>]{[(1+1)][a-L-Rhap]{[(3+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 626 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6 / Details: 20 mM MES pH 6.0, 50 mM sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.90137 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90137 Å / Relative weight: 1
ReflectionResolution: 1.5→84.53 Å / Num. obs: 103277 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.041 / Rrim(I) all: 0.134 / Χ2: 0.92 / Net I/σ(I): 14.1
Reflection shell

% possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
8.22-84.5320.30.02861.166610.0090.0290.4
1.5-1.5320.72.5841.351080.6690.8432.7180.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→69.172 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.357 / SU ML: 0.037 / Cross valid method: FREE R-VALUE / ESU R: 0.052 / ESU R Free: 0.05
Details: Hydrogens have not been used. There is a region of unmodelled density between the side chains of Phe219, Val227 and Glu228. There is also unmodelled density between the side chains of Phe208, Tyr239 and Leu288.
RfactorNum. reflection% reflection
Rfree0.1596 5069 4.914 %
Rwork0.1306 98087 -
all0.132 --
obs-103156 99.947 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.048 Å2
Baniso -1Baniso -2Baniso -3
1-0.418 Å20.209 Å20 Å2
2--0.418 Å2-0 Å2
3----1.356 Å2
Refinement stepCycle: LAST / Resolution: 1.5→69.172 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3293 0 87 626 4006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0123602
X-RAY DIFFRACTIONr_angle_refined_deg1.8271.8094925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.233528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95210561
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.76810163
X-RAY DIFFRACTIONr_chiral_restr0.1280.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022841
X-RAY DIFFRACTIONr_nbd_refined0.2410.21791
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22407
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2555
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1610.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2020.216
X-RAY DIFFRACTIONr_mcbond_it5.011.9611721
X-RAY DIFFRACTIONr_mcangle_it6.7573.5352174
X-RAY DIFFRACTIONr_scbond_it7.7452.2081881
X-RAY DIFFRACTIONr_scangle_it10.3243.9592751
X-RAY DIFFRACTIONr_lrange_it15.18825.3045985
X-RAY DIFFRACTIONr_rigid_bond_restr5.5333602
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.5-1.5390.2553830.24372000.24375960.9480.95699.82890.233
1.539-1.5810.2393500.21570910.21674470.9610.96899.91940.201
1.581-1.6270.2223260.19568990.19672330.9690.97599.88940.176
1.627-1.6770.1953880.17365790.17469730.9760.98199.9140.153
1.677-1.7320.2163080.15864640.1667770.9740.98599.92620.137
1.732-1.7930.1993150.14162600.14465780.9770.98899.95440.12
1.793-1.860.1673120.11960640.12163770.9840.99199.98430.1
1.86-1.9360.1473050.10357960.10561080.9880.99399.88540.088
1.936-2.0220.142800.10155690.10358510.9890.99499.96580.09
2.022-2.1210.1472820.10753400.10956240.9870.99499.96440.097
2.121-2.2350.1462610.10750340.10952960.9880.99499.98110.099
2.235-2.3710.1552410.10748190.10950600.9860.9931000.097
2.371-2.5340.1562080.1145410.11247490.9860.9931000.101
2.534-2.7370.1632060.11942030.12144090.9840.9911000.111
2.737-2.9980.1511950.1238760.12140710.9860.9911000.113
2.998-3.3510.1412110.13135040.13237150.9880.991000.125
3.351-3.8680.1381630.12530760.12632390.9890.9921000.122
3.868-4.7330.1251460.10726070.10827530.9920.9931000.105
4.733-6.6780.1591310.15620180.15621490.9880.991000.153
6.678-69.1720.217580.21511470.21512050.9830.9751000.209

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