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- PDB-8b5s: Crystal Structure of P. aeruginosa WaaG in complex with UDP-glucose -

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Basic information

Entry
Database: PDB / ID: 8b5s
TitleCrystal Structure of P. aeruginosa WaaG in complex with UDP-glucose
Components(UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG) x 2
KeywordsTRANSFERASE / WaaG / glycosyltransferase
Function / homology: / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / lipopolysaccharide biosynthetic process / glycosyltransferase activity / nucleotide binding / URIDINE-5'-DIPHOSPHATE / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsScaletti, E. / Gustafsson Westergren, R. / Stenmark, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural and functional insights into the Pseudomonas aeruginosa glycosyltransferase WaaG and the implications for lipopolysaccharide biosynthesis.
Authors: Scaletti, E.R. / Pettersson, P. / Patrick, J. / Shilling, P.J. / Westergren, R.G. / Daley, D.O. / Maler, L. / Widmalm, G. / Stenmark, P.
History
DepositionSep 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
B: UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1174
Polymers84,1462
Non-polymers9702
Water11,656647
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-15 kcal/mol
Surface area31600 Å2
Unit cell
Length a, b, c (Å)58.633, 94.426, 70.170
Angle α, β, γ (deg.)90.00, 101.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG


Mass: 42282.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: waaG / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HUF6
#2: Protein UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG


Mass: 41863.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: waaG, PA5010 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HUF6
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 647 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.06M Divalents, 0.1M Buffer System 3 pH 8.5, 30.0% v/v P500MME_P20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.95→57.551 Å / Num. obs: 182700 / % possible obs: 99.9 % / Redundancy: 3.4 % / CC1/2: 0.979 / Net I/σ(I): 10
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3796 / CC1/2: 0.979

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IV7

2iv7


Resolution: 1.95→57.54 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.936 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21905 2794 5.1 %RANDOM
Rwork0.1797 ---
obs0.18173 51684 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.148 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å20 Å2-0.85 Å2
2--0.7 Å20 Å2
3----0.53 Å2
Refinement stepCycle: 1 / Resolution: 1.95→57.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5822 0 0 647 6469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0126037
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165491
X-RAY DIFFRACTIONr_angle_refined_deg0.871.6498209
X-RAY DIFFRACTIONr_angle_other_deg0.3121.56112759
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.541565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75610975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6581.722941
X-RAY DIFFRACTIONr_mcbond_other0.6551.7192940
X-RAY DIFFRACTIONr_mcangle_it1.1392.5723685
X-RAY DIFFRACTIONr_mcangle_other1.1392.5723686
X-RAY DIFFRACTIONr_scbond_it0.8141.8623096
X-RAY DIFFRACTIONr_scbond_other0.8141.8623097
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3832.7524525
X-RAY DIFFRACTIONr_long_range_B_refined3.44325.8776878
X-RAY DIFFRACTIONr_long_range_B_other3.0823.8596664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 224 -
Rwork0.226 3747 -
obs--99.13 %

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