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- PDB-6y6g: lipopolysaccharide outer core galactosyltransferase WaaB apo form -

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Basic information

Entry
Database: PDB / ID: 6y6g
Titlelipopolysaccharide outer core galactosyltransferase WaaB apo form
ComponentsLipopolysaccharide 1,6-galactosyltransferase
KeywordsBIOSYNTHETIC PROTEIN / WaaB / lipopolysaccharide / galactosyltransferase / lipopolysaccharide outer core
Function / homologyGlycosyltransferase Family 4 / Glycosyltransferase subfamily 4-like, N-terminal domain / lipopolysaccharide core region biosynthetic process / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / Lipopolysaccharide 1,6-galactosyltransferase
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipopolysaccharide 1,6-galactosyltransferase


Theoretical massNumber of molelcules
Total (without water)40,9431
Polymers40,9431
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15870 Å2
Unit cell
Length a, b, c (Å)104.270, 104.270, 88.440
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-407-

HOH

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Components

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


Mass: 40943.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: WaaB
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Gene: rfaB, waaB, STM3719
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q06994, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.94 Å3/Da / Density % sol: 58.1 %
Crystal growTemperature: 297 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: 1.823 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Feb 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.823 Å / Relative weight: 1
ReflectionResolution: 1.81→67.54 Å / Num. obs: 44277 / % possible obs: 98.5 % / Redundancy: 60.1 % / CC1/2: 1 / Rmerge(I) obs: 0.125 / Net I/σ(I): 29
Reflection shellResolution: 1.81→1.875 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.863 / Num. unique obs: 3879 / CC1/2: 0.6 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→67.54 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.65 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.146 / ESU R Free: 0.099
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 2225 5 %RANDOM
Rwork0.163 ---
obs0.1646 42052 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 106.01 Å2 / Biso mean: 30.493 Å2 / Biso min: 16.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å20 Å2
2---1.11 Å20 Å2
3---2.21 Å2
Refinement stepCycle: final / Resolution: 1.81→67.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 0 327 3164
Biso mean---43.96 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132912
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172678
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.6323940
X-RAY DIFFRACTIONr_angle_other_deg1.291.5746217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7075356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.21622.766141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6441512
X-RAY DIFFRACTIONr_chiral_restr0.0810.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02634
X-RAY DIFFRACTIONr_rigid_bond_restr0.54935590
LS refinement shellResolution: 1.81→1.857 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 138 -
Rwork0.317 2660 -
all-2798 -
obs--85.41 %
Refinement TLS params.Method: refined / Origin x: 106.3279 Å / Origin y: 130.3869 Å / Origin z: 91.3015 Å
111213212223313233
T0.0334 Å20.0187 Å2-0.0179 Å2-0.0555 Å2-0.034 Å2--0.025 Å2
L0.5822 °2-0.09 °20.3266 °2-0.0465 °2-0.1336 °2--0.4154 °2
S-0.0759 Å °-0.0937 Å °0.0983 Å °0.0019 Å °0.021 Å °-0.0179 Å °-0.0261 Å °-0.046 Å °0.0549 Å °

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