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Open data
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Basic information
Entry | Database: PDB / ID: 9g17 | ||||||
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Title | Structure of PslG with a covalently- bound pentasaccharide | ||||||
![]() | PslG | ||||||
![]() | HYDROLASE / endo-glucanase / activity-based probe / epoxide | ||||||
Function / homology | : / polysaccharide biosynthetic process / single-species biofilm formation / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / PslG![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Offen, W.A. / Davies, G.J. | ||||||
Funding support | European Union, 1items
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 271.1 KB | Display | ![]() |
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PDB format | ![]() | 176.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 793.3 KB | Display | ![]() |
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Full document | ![]() | 796.8 KB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 41.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9g18C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | 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.) ![]() ![]() ![]() ![]() |
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#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)-(1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol Type: oligosaccharide / Mass: 826.745 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 4 types, 642 molecules 






#3: Chemical | #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.29 % |
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Crystal grow | Temperature: 277 K / Method: batch mode / pH: 6 / Details: 20 mM MES pH 6.0, 50 mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 6, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95392 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() 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.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.288 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→84.604 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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