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- PDB-9g17: Structure of PslG with a covalently- bound pentasaccharide -

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Basic information

Entry
Database: PDB / ID: 9g17
TitleStructure of PslG with a covalently- bound pentasaccharide
ComponentsPslG
KeywordsHYDROLASE / endo-glucanase / activity-based probe / epoxide
Function / homology: / single-species biofilm formation / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / Chem-YLL / PslG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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
Revision 2.0Apr 8, 2026Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _chem_comp_bond.comp_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_modification_feature.auth_asym_id / _pdbx_modification_feature.auth_comp_id / _pdbx_modification_feature.auth_seq_id / _pdbx_modification_feature.category / _pdbx_modification_feature.label_asym_id / _pdbx_modification_feature.label_comp_id / _pdbx_modification_feature.ref_comp_id / _pdbx_modification_feature.ref_pcm_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id

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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)48,90713
Polymers47,3811
Non-polymers1,52712
Water11,385632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-23 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.692, 97.692, 119.775
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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-rhamnopyranose


Type: oligosaccharide / Mass: 650.578 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-2DManpb1-3DManpb1-3LRhapa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2211m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-2-3/a3-b1_b3-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][L-1-deoxy-Rhap]{[(3+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 643 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-YLL / (1R,2S,3S,4S,5R,6R)-6-(HYDROXYMETHYL)CYCLOHEXANE-1,2,3,4,5-PENTOL


Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.44 Å3/Da / Density % sol: 64.29 %
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: 0.95392 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95392 Å / Relative weight: 1
ReflectionResolution: 1.55→84.604 Å / Num. obs: 93736 / % possible obs: 100 % / Redundancy: 16.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.057 / Net I/σ(I): 11
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 16.2 % / Num. unique obs: 4675 / CC1/2: 0.663 / Rpim(I) all: 0.926 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.82)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→84.604 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.937 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.06
Details: The YLL moiety of the ligand has 2 conformations which are covalently bound to 2 distinct conformations of the Glu276 side chain. The side chain of Tyr239 is modelled with 3 partially ...Details: The YLL moiety of the ligand has 2 conformations which are covalently bound to 2 distinct conformations of the Glu276 side chain. The side chain of Tyr239 is modelled with 3 partially occupied conformations. There are regions of unmodelled electron density between the side chains of Phe219, Glu228 and Leu264, and also between the side chains of Leu54 and Arg84, and at the N-terminus of the protein.
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 4697 5.014 %RANDOM
Rwork0.1419 88986 --
all0.143 ---
obs-93683 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: 23.288 Å2
Baniso -1Baniso -2Baniso -3
1-0.361 Å20.181 Å20 Å2
2--0.361 Å2-0 Å2
3----1.171 Å2
Refinement stepCycle: LAST / Resolution: 1.55→84.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 95 632 4036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123765
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.8165165
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3325460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.766531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11910587
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.04110176
X-RAY DIFFRACTIONr_chiral_restr0.1260.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022991
X-RAY DIFFRACTIONr_nbd_refined0.2050.21893
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2587
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.190.244
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.211
X-RAY DIFFRACTIONr_mcbond_it4.4521.8921771
X-RAY DIFFRACTIONr_mcangle_it6.0773.4042254
X-RAY DIFFRACTIONr_scbond_it7.0842.1251994
X-RAY DIFFRACTIONr_scangle_it9.5173.7912911
X-RAY DIFFRACTIONr_lrange_it15.42923.8216275
X-RAY DIFFRACTIONr_rigid_bond_restr5.22533765
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
1.55-1.590.2823620.26365380.26469160.940.9599.76870.265
1.59-1.6340.2783040.24464300.24667340.9520.9591000.244
1.634-1.6810.2543520.21862110.2265630.9560.9691000.216
1.681-1.7330.233260.19760080.19963340.9690.9771000.192
1.733-1.790.1963160.17758890.17862050.9770.9811000.168
1.79-1.8520.2023150.1556390.15359540.9750.9861000.138
1.852-1.9220.1782540.12855140.1357680.9810.9891000.115
1.922-2.0010.1562560.11352940.11555500.9840.9931000.102
2.001-2.090.1582880.11550290.11753180.9850.99399.98120.106
2.09-2.1920.1442750.11448070.11650820.9870.9941000.107
2.192-2.310.1732430.11545840.11848270.9840.9931000.107
2.31-2.450.1422350.11243680.11446040.9890.99399.97830.103
2.45-2.6190.1632500.11940570.12143070.9830.9921000.109
2.619-2.8290.1631980.12337900.12639880.9850.9911000.115
2.829-3.0980.161760.12635280.12737040.9840.9911000.117
3.098-3.4640.1461590.1331940.13133530.990.9911000.124
3.464-3.9980.1421400.12128180.12229580.9890.9921000.117
3.998-4.8940.1441140.1223950.12125090.990.9931000.116
4.894-6.910.228970.19518410.19719390.9860.98999.94840.191
6.91-84.6040.284370.2610520.26110920.9840.9799.72530.257

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