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- PDB-8b62: Crystal Structure of P. aeruginosa WaaG in complex with UDP-galactose -

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Basic information

Entry
Database: PDB / ID: 8b62
TitleCrystal Structure of P. aeruginosa WaaG in complex with UDP-galactose
ComponentsUDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
KeywordsTRANSFERASE / glycosyltransferase / WaaG
Function / homology: / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / lipopolysaccharide biosynthetic process / glycosyltransferase activity / nucleotide binding / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)85,2155
Polymers83,9902
Non-polymers1,2253
Water7,134396
1
A: UDP-glucose:(Heptosyl) LPS alpha 1,3-glucosyltransferase WaaG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6533
Polymers41,9951
Non-polymers6582
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)42,5612
Polymers41,9951
Non-polymers5661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.980, 109.750, 94.620
Angle α, β, γ (deg.)90.00, 90.01, 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-GDU / GALACTOSE-URIDINE-5'-DIPHOSPHATE / UDP-D-GALACTOPYRANOSE


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M PCTP pH 6.0, 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: 2.02→47.5 Å / Num. obs: 55384 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 2.02→2.06 Å / Num. unique obs: 2657 / CC1/2: 0.788

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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: 2.02→47.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.985 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22013 2723 4.9 %RANDOM
Rwork0.17376 ---
obs0.17601 52635 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.204 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å2-0 Å2-0.27 Å2
2--0.58 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 2.02→47.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5844 0 0 396 6240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165500
X-RAY DIFFRACTIONr_angle_refined_deg1.51.658174
X-RAY DIFFRACTIONr_angle_other_deg0.5071.5612776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.883567
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89710976
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021272
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_it2.3413.0412921
X-RAY DIFFRACTIONr_mcbond_other2.3423.0412920
X-RAY DIFFRACTIONr_mcangle_it3.0774.5433653
X-RAY DIFFRACTIONr_mcangle_other3.0774.5443654
X-RAY DIFFRACTIONr_scbond_it3.513.4573098
X-RAY DIFFRACTIONr_scbond_other3.513.4583099
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2085.0434522
X-RAY DIFFRACTIONr_long_range_B_refined6.72441.8936670
X-RAY DIFFRACTIONr_long_range_B_other6.66140.6196586
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.023→2.075 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 182 -
Rwork0.238 3817 -
obs--97.04 %

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