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- PDB-6y6i: lipopolysaccharide outer core galactosyltransferase WaaB and UDP ... -

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Basic information

Entry
Database: PDB / ID: 6y6i
Titlelipopolysaccharide outer core galactosyltransferase WaaB and UDP complex
ComponentsLipopolysaccharide 1,6-galactosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / WaaB / lipopolysaccharide / galactosyltransferase / UDP / lipopolysaccharide outer core
Function / homologyGlycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / lipopolysaccharide core region biosynthetic process / Glycosyl transferases group 1 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / URIDINE-5'-DIPHOSPHATE / Lipopolysaccharide 1,6-galactosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsZhang, Z.Y. / Ashworth, G. / Wang, Z.S. / Zhu, X.F. / Dong, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT106121MA United Kingdom
CitationJournal: To Be Published
Title: Structural insights into the lipopolysaccharide outer core galactosyltransferase WaaB
Authors: Zhang, Z.Y. / Ashworth, G. / Wang, Z.S. / Zhu, X.F. / Dong, C.J.
History
DepositionFeb 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide 1,6-galactosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4752
Polymers41,0711
Non-polymers4041
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area540 Å2
ΔGint-3 kcal/mol
Surface area15790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.440, 104.440, 89.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

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Components

#1: Protein Lipopolysaccharide 1,6-galactosyltransferase / UDP-D-galactose--(Glucosyl)lipopolysaccharide-alpha-1 / 3-D-galactosyltransferase


Mass: 41071.301 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: rfaB, waaB, STM3719 / Production host: Escherichia coli (E. coli)
References: UniProt: Q06994, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#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

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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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% tryptone, 1mM sodium azide, 0.05M HEPES pH7.0 and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 81 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→73.85 Å / Num. obs: 38400 / % possible obs: 99.9 % / Redundancy: 23.4 % / CC1/2: 1 / Rmerge(I) obs: 0.16 / Net I/σ(I): 16.1
Reflection shellResolution: 1.92→1.989 Å / Redundancy: 11.8 % / Rmerge(I) obs: 1.33 / Num. unique obs: 3752 / CC1/2: 0.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y6G

6y6g


Resolution: 1.92→73.85 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 8.067 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2134 1978 5.2 %RANDOM
Rwork0.1635 ---
obs0.1662 36421 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.3 Å2 / Biso mean: 33.397 Å2 / Biso min: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2--2.61 Å20 Å2
3----5.22 Å2
Refinement stepCycle: final / Resolution: 1.92→73.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2849 0 25 326 3200
Biso mean--54.37 45.04 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132950
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172708
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.6463994
X-RAY DIFFRACTIONr_angle_other_deg1.3521.5796291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2085357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22722.766141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5041512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023250
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
X-RAY DIFFRACTIONr_rigid_bond_restr0.96535658
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 153 -
Rwork0.295 2611 -
all-2764 -
obs--99.39 %
Refinement TLS params.Method: refined / Origin x: -26.5 Å / Origin y: 2.321 Å / Origin z: -19.749 Å
111213212223313233
T0.0424 Å2-0.0027 Å20.0363 Å2-0.0084 Å2-0.0065 Å2--0.2281 Å2
L0.0163 °2-0.0198 °20.0201 °2-0.5446 °20.3891 °2--0.5915 °2
S0.0123 Å °0.0072 Å °0.0343 Å °0.0746 Å °-0.043 Å °0.0511 Å °0.0296 Å °-0.0096 Å °0.0307 Å °

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