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- PDB-8x4m: Crystal structure of the glycosyltransferase domain of Legionella... -

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Basic information

Entry
Database: PDB / ID: 8x4m
TitleCrystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPD
ComponentsSubversion of eukaryotic traffic protein A
KeywordsTRANSFERASE / Glycosyltransferase activity Catalytic activity
Function / homology
Function and homology information


mannosyl-inositol phosphorylceramide biosynthetic process / mannosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / extracellular region / membrane
Similarity search - Function
: / Glycosyltransferase, DXD sugar-binding motif / Glycosyltransferase sugar-binding region containing DXD motif / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Subversion of eukaryotic traffic protein A
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsIm, H.N. / Lee, Y. / Jang, D.M. / Hahn, H. / Kim, H.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPD
Authors: Im, H.N. / Lee, Y. / Jang, D.M. / Hahn, H. / Kim, H.S.
History
DepositionNov 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Subversion of eukaryotic traffic protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3598
Polymers52,5901
Non-polymers7697
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.823, 62.795, 176.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Subversion of eukaryotic traffic protein A


Mass: 52589.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: setA / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZU30

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Non-polymers , 5 types, 296 molecules

#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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 6% (v/v) MPD, 14% (w/v) PEG 4,000, and 0.1 M sodium/potassium phosphate at pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.79→29.6 Å / Num. obs: 44091 / % possible obs: 98.6 % / Redundancy: 4.86 % / Rsym value: 0.132 / Net I/σ(I): 15.5
Reflection shellResolution: 1.79→1.9 Å / Num. unique obs: 2190 / Rpim(I) all: 0.463

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→29.6 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.404 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22814 2094 4.8 %RANDOM
Rwork0.20054 ---
obs0.20185 41930 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.524 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å2-0 Å2
2---0.92 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: 1 / Resolution: 1.79→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 0 48 289 3970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123759
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163436
X-RAY DIFFRACTIONr_angle_refined_deg0.831.6465087
X-RAY DIFFRACTIONr_angle_other_deg0.3011.5648054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.79516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90210675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2555
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024164
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
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_it1.1462.8211803
X-RAY DIFFRACTIONr_mcbond_other1.1452.8211803
X-RAY DIFFRACTIONr_mcangle_it2.0114.2272252
X-RAY DIFFRACTIONr_mcangle_other2.0114.2292253
X-RAY DIFFRACTIONr_scbond_it1.1262.9421956
X-RAY DIFFRACTIONr_scbond_other1.1262.9431957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9074.3522836
X-RAY DIFFRACTIONr_long_range_B_refined4.13838.3594315
X-RAY DIFFRACTIONr_long_range_B_other4.05337.3364259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.839 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 145 -
Rwork0.269 2798 -
obs--90.69 %

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