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- PDB-8x4j: Crystal structure of the glycosyltransferase domain of Legionella... -

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Basic information

Entry
Database: PDB / ID: 8x4j
TitleCrystal structure of the glycosyltransferase domain of Legionella SetA (unbound)
ComponentsSubversion of eukaryotic traffic protein A
KeywordsTRANSFERASE / Glycosyltransferase 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
Subversion of eukaryotic traffic protein A
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.54 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 Legionella effector SetA glycosyltransferase domain in the unbound form
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)53,8112
Polymers53,7871
Non-polymers241
Water97354
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)139.413, 139.413, 59.944
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Subversion of eukaryotic traffic protein A


Mass: 53786.953 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.13 Å3/Da / Density % sol: 60.66 %
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: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.54→42.57 Å / Num. obs: 21215 / % possible obs: 99.9 % / Redundancy: 5.5 % / Rsym value: 0.01 / Net I/σ(I): 48.1
Reflection shellResolution: 2.54→2.63 Å / Rmerge(I) obs: 0.01 / Num. unique obs: 21215

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.54→42.57 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.995 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.374 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24681 1079 4.8 %RANDOM
Rwork0.19349 ---
obs0.19617 21215 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.897 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å2-0 Å2
3----2.79 Å2
Refinement stepCycle: 1 / Resolution: 2.54→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 1 54 3663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163389
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.6454999
X-RAY DIFFRACTIONr_angle_other_deg0.3611.5687940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.183516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35910671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0490.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02694
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_it4.0436.9371781
X-RAY DIFFRACTIONr_mcbond_other4.0436.9371781
X-RAY DIFFRACTIONr_mcangle_it6.18710.3952221
X-RAY DIFFRACTIONr_mcangle_other6.18510.3972222
X-RAY DIFFRACTIONr_scbond_it4.2917.3611912
X-RAY DIFFRACTIONr_scbond_other4.297.3631913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.77610.892779
X-RAY DIFFRACTIONr_long_range_B_refined9.25180.9444058
X-RAY DIFFRACTIONr_long_range_B_other9.2580.9434059
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.542→2.608 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 82 -
Rwork0.257 1534 -
obs--98.96 %

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