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- PDB-8b63: Crystal Structure of P. aeruginosa WaaG in complex with UDP-GalNAc -

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Basic information

Entry
Database: PDB / ID: 8b63
TitleCrystal Structure of P. aeruginosa WaaG in complex with UDP-GalNAc
ComponentsUDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
KeywordsTRANSFERASE / glycosyltransferase / WaaG
Function / homology
Function and homology information


lipopolysaccharide biosynthetic process / glycosyltransferase activity / nucleotide binding
Similarity search - Function
: / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
ACETATE ION / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / URIDINE-5'-DIPHOSPHATE / UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 25, 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)85,0615
Polymers83,9902
Non-polymers1,0713
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-11 kcal/mol
Surface area31650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.762, 109.963, 94.326
Angle α, β, γ (deg.)90.00, 90.22, 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-UD2 / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / (2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M MIB pH 4.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→55.042 Å / Num. obs: 43178 / % possible obs: 99.9 % / Redundancy: 4.9 % / CC1/2: 0.991 / Net I/σ(I): 5.5
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 3679 / CC1/2: 0.554

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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: 2.2→55.04 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.317 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25814 2152 5 %RANDOM
Rwork0.21898 ---
obs0.22105 40977 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.501 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å20 Å2-0.67 Å2
2--1.18 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.2→55.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 68 94 5943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126025
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165494
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.658185
X-RAY DIFFRACTIONr_angle_other_deg0.5211.5612750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.561568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00110971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.2892
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021274
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_it3.2893.8242938
X-RAY DIFFRACTIONr_mcbond_other3.2893.8232937
X-RAY DIFFRACTIONr_mcangle_it4.6165.7213673
X-RAY DIFFRACTIONr_mcangle_other4.6155.7213674
X-RAY DIFFRACTIONr_scbond_it3.9454.2243087
X-RAY DIFFRACTIONr_scbond_other3.9444.2263080
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8356.1854513
X-RAY DIFFRACTIONr_long_range_B_refined7.71448.1626540
X-RAY DIFFRACTIONr_long_range_B_other7.71448.1636535
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 146 -
Rwork0.294 2956 -
obs--98.88 %

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