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- PDB-8x4n: Crystal structure of the PI3P-binding domain of Legionella SetA i... -

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Basic information

Entry
Database: PDB / ID: 8x4n
TitleCrystal structure of the PI3P-binding domain of Legionella SetA in complex with inositol 1,3-bisphosphate
ComponentsSubversion of eukaryotic traffic protein A
KeywordsTRANSFERASE / Glycosyltransferase activity lipid-binding protein
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
Chem-ITP / Subversion of eukaryotic traffic protein A
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 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 PI3P-binding domain of Legionella SetA in complex with inositol 1,3-bisphosphate
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,1614
Polymers28,7282
Non-polymers4322
Water1,69394
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)113.247, 36.915, 72.407
Angle α, β, γ (deg.)90.00, 111.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Subversion of eukaryotic traffic protein A


Mass: 14364.172 Da / Num. of mol.: 2
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ITP / PHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER / INOSITOL 1,3-BISPHOSPHATE


Mass: 340.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O12P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) polyacrylic acid 5,100, 0.1 M HEPES pH 7.0, and 20 mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.46→29.52 Å / Num. obs: 10267 / % possible obs: 99.1 % / Redundancy: 3.86 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 21.5
Reflection shellResolution: 2.46→2.55 Å / Num. unique obs: 478 / Rpim(I) all: 0.437

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.46→29.52 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.086 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.455 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25322 517 5 %RANDOM
Rwork0.20493 ---
obs0.20737 9749 98.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.111 Å2
Baniso -1Baniso -2Baniso -3
1-5.07 Å2-0 Å2-2.59 Å2
2---0.5 Å2-0 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Resolution: 2.46→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1727 0 26 94 1847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0121776
X-RAY DIFFRACTIONr_bond_other_d0.0020.0161646
X-RAY DIFFRACTIONr_angle_refined_deg0.8591.6532390
X-RAY DIFFRACTIONr_angle_other_deg0.2971.5763846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9895215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.86459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73110330
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0380.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021976
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
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_it2.094.206869
X-RAY DIFFRACTIONr_mcbond_other2.094.206869
X-RAY DIFFRACTIONr_mcangle_it3.686.2851081
X-RAY DIFFRACTIONr_mcangle_other3.6786.2891082
X-RAY DIFFRACTIONr_scbond_it2.354.484907
X-RAY DIFFRACTIONr_scbond_other2.3494.481908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2026.5991310
X-RAY DIFFRACTIONr_long_range_B_refined6.46953.7011956
X-RAY DIFFRACTIONr_long_range_B_other6.44953.7241949
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.46→2.523 Å
RfactorNum. reflection% reflection
Rfree0.385 34 -
Rwork0.301 621 -
obs--90.22 %

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