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- PDB-9pfa: Crystal structure of the glycosyltransferase SvFucT from Saponari... -

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Basic information

Entry
Database: PDB / ID: 9pfa
TitleCrystal structure of the glycosyltransferase SvFucT from Saponaria vaccaria
Componentsglycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyURIDINE-5'-DIPHOSPHATE
Function and homology information
Biological speciesGypsophila vaccaria (cowherb)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsPereira, J.H. / Hudson, G.A. / Keasling, J.D. / Adams, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: Jacs Au / Year: 2025
Title: Enzymology and Structural Basis of Glycosyltransferases Involved in Saponin C28 Carboxylic Acid O ‐d‐Fucosylation.
Authors: Hudson, G.A. / Pereira, J.H. / Winegar, P.H. / FitzGerald, D.M. / DeGiovanni, A. / Chen, X. / Zhao, X. / Astolfi, M.C.T. / Reed, J. / El-Demerdash, A. / Rejzek, M. / Kikuchi, S. / Osbourn, A. ...Authors: Hudson, G.A. / Pereira, J.H. / Winegar, P.H. / FitzGerald, D.M. / DeGiovanni, A. / Chen, X. / Zhao, X. / Astolfi, M.C.T. / Reed, J. / El-Demerdash, A. / Rejzek, M. / Kikuchi, S. / Osbourn, A. / Scheller, H.V. / Adams, P.D. / Keasling, J.D.
History
DepositionJul 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glycosyltransferase
B: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,4378
Polymers106,5312
Non-polymers9066
Water15,025834
1
A: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7184
Polymers53,2661
Non-polymers4533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7184
Polymers53,2661
Non-polymers4533
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.564, 110.730, 170.548
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein glycosyltransferase


Mass: 53265.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gypsophila vaccaria (cowherb) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 834 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 6.5 25 % (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→48.48 Å / Num. obs: 91222 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.999 / Net I/σ(I): 11.8
Reflection shellResolution: 1.74→1.8 Å / Num. unique obs: 7425 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→48.48 Å / SU ML: 0.2181 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 21.5409
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 1840 2.02 %
Rwork0.1749 89378 -
obs0.1756 91218 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.41 Å2
Refinement stepCycle: LAST / Resolution: 1.74→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 4 834 8118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01287462
X-RAY DIFFRACTIONf_angle_d1.024710148
X-RAY DIFFRACTIONf_chiral_restr0.06511132
X-RAY DIFFRACTIONf_plane_restr0.01171298
X-RAY DIFFRACTIONf_dihedral_angle_d15.43412691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.790.35921160.31335571X-RAY DIFFRACTION75.73
1.79-1.840.37921190.27855905X-RAY DIFFRACTION80.23
1.84-1.90.27661270.24666188X-RAY DIFFRACTION83.95
1.9-1.970.25631360.21816454X-RAY DIFFRACTION87.47
1.97-2.050.23881370.18946701X-RAY DIFFRACTION90.21
2.05-2.140.2311400.17746919X-RAY DIFFRACTION93.13
2.14-2.250.17451460.16237017X-RAY DIFFRACTION94.8
2.25-2.390.21491440.16597175X-RAY DIFFRACTION96.29
2.39-2.580.19591490.1677238X-RAY DIFFRACTION97.07
2.58-2.840.23481550.16837346X-RAY DIFFRACTION98.14
2.84-3.250.22091520.17277434X-RAY DIFFRACTION98.98
3.25-4.090.1931560.14867567X-RAY DIFFRACTION99.61
4.09-48.480.16861630.16817863X-RAY DIFFRACTION99.58

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