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- PDB-8b5q: Crystal Structure of P. aeruginosa WaaG in complex with UMP -

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Basic information

Entry
Database: PDB / ID: 8b5q
TitleCrystal Structure of P. aeruginosa WaaG in complex with UMP
ComponentsUDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
KeywordsTRANSFERASE / WaaG / glycosyltransferase
Function / homologyGlycosyl transferase, family 1 / Glycosyl transferases group 1 / lipopolysaccharide biosynthetic process / glycosyltransferase activity / nucleotide binding / URIDINE-5'-MONOPHOSPHATE / UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 2.0Dec 17, 2025Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme
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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.mon_nstd_flag / _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 / _chem_comp_bond.value_order / _pdbx_entity_nonpoly.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id

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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)84,6394
Polymers83,9902
Non-polymers6482
Water5,873326
1
A: UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3192
Polymers41,9951
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3192
Polymers41,9951
Non-polymers3241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.928, 108.441, 92.358
Angle α, β, γ (deg.)90.00, 90.11, 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: 41995.074 Da / Num. of mol.: 2
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: Chemical ChemComp-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium chloride, 0.1 M MES pH 6.0, 20 % PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→108.4 Å / Num. obs: 53974 / % possible obs: 96.9 % / Redundancy: 3.3 % / CC1/2: 0.911 / Net I/σ(I): 6.6
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 4041 / CC1/2: 0.36

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Processing

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

2iv7


Resolution: 2→92.36 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.032 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24461 2666 4.9 %RANDOM
Rwork0.19413 ---
obs0.19663 51278 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.409 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å20.67 Å2
2--2.14 Å20 Å2
3----0.56 Å2
Refinement stepCycle: 1 / Resolution: 2→92.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5842 0 0 326 6168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126036
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165518
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6498197
X-RAY DIFFRACTIONr_angle_other_deg0.5291.5612808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4615739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.266569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25910983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2889
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021286
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_it3.2153.8022947
X-RAY DIFFRACTIONr_mcbond_other3.2153.8022946
X-RAY DIFFRACTIONr_mcangle_it4.1965.6883689
X-RAY DIFFRACTIONr_mcangle_other4.1955.6883690
X-RAY DIFFRACTIONr_scbond_it4.2214.2493089
X-RAY DIFFRACTIONr_scbond_other4.224.2483090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9476.2154509
X-RAY DIFFRACTIONr_long_range_B_refined7.22949.7286611
X-RAY DIFFRACTIONr_long_range_B_other7.23449.4346571
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 246 -
Rwork0.285 3790 -
obs--99.68 %

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