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- PDB-9pf3: Crystal structure of the glycosyltransferase QsFucT from Quillaja... -

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Basic information

Entry
Database: PDB / ID: 9pf3
TitleCrystal structure of the glycosyltransferase QsFucT from Quillaja saponaria
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / glycosyltransferase
Function / homologyquercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesQuillaja saponaria (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6152
Polymers51,2101
Non-polymers4041
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.237, 76.552, 58.975
Angle α, β, γ (deg.)90.000, 115.398, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycosyltransferase


Mass: 51210.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Quillaja saponaria (plant) / Gene: O6P43_026350 / Production host: Escherichia coli (E. coli)
References: UniProt: A0AAD7L3C9, Transferases; Glycosyltransferases; Hexosyltransferases
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M BIS-Tris pH 5.5 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: 8.2.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→48.15 Å / Num. obs: 48854 / % possible obs: 99.14 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.83 Å2 / CC1/2: 0.996 / Net I/σ(I): 7.6
Reflection shellResolution: 2.11→2.18 Å / Num. unique obs: 2538 / CC1/2: 0.32

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→48.15 Å / SU ML: 0.3044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.7421
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 3820 7.82 %
Rwork0.2071 45034 -
obs0.2093 48854 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.93 Å2
Refinement stepCycle: LAST / Resolution: 2.11→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 25 99 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273501
X-RAY DIFFRACTIONf_angle_d0.51954752
X-RAY DIFFRACTIONf_chiral_restr0.0417528
X-RAY DIFFRACTIONf_plane_restr0.0042598
X-RAY DIFFRACTIONf_dihedral_angle_d17.34881259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.140.39671360.3581644X-RAY DIFFRACTION94.83
2.14-2.160.33251150.33091660X-RAY DIFFRACTION97.8
2.16-2.190.35051560.32651704X-RAY DIFFRACTION97.28
2.19-2.230.30041470.32521631X-RAY DIFFRACTION97
2.23-2.260.33641220.31171709X-RAY DIFFRACTION97.81
2.26-2.290.35751750.31511619X-RAY DIFFRACTION97.08
2.29-2.330.30941150.29221687X-RAY DIFFRACTION97.09
2.33-2.370.33991760.2971636X-RAY DIFFRACTION98
2.37-2.420.33191300.27031709X-RAY DIFFRACTION97.3
2.42-2.460.31961450.27021699X-RAY DIFFRACTION98.35
2.46-2.510.27291620.26181631X-RAY DIFFRACTION97.5
2.51-2.570.25941330.26521720X-RAY DIFFRACTION98.51
2.57-2.630.28221490.24791673X-RAY DIFFRACTION98.33
2.63-2.690.27441360.2471678X-RAY DIFFRACTION98.27
2.69-2.760.27621560.23731670X-RAY DIFFRACTION97.91
2.76-2.850.24841290.23741694X-RAY DIFFRACTION98.81
2.85-2.940.25621480.23031705X-RAY DIFFRACTION98.2
2.94-3.040.24251330.21981677X-RAY DIFFRACTION98.05
3.04-3.160.23581400.21251652X-RAY DIFFRACTION97.34
3.17-3.310.22691480.1991665X-RAY DIFFRACTION98.16
3.31-3.480.24111470.19141684X-RAY DIFFRACTION96.98
3.48-3.70.18761370.17321655X-RAY DIFFRACTION96.5
3.7-3.990.19711410.16871627X-RAY DIFFRACTION95.46
3.99-4.390.18721450.1561659X-RAY DIFFRACTION96.73
4.39-5.020.17921240.14681653X-RAY DIFFRACTION95.59
5.02-6.320.18381400.17331650X-RAY DIFFRACTION96.6
6.33-48.150.20841350.17491643X-RAY DIFFRACTION95.23
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.874793974420.4188059731790.8120431929265.693278938390.738279182063.96002138015-0.09710836553920.05516459834520.151607740315-0.03974940186630.03004698999550.0688424628414-0.4374901029740.01363322747090.0823940384670.325363035919-0.0145924309488-0.04637550804840.289130560969-0.02692317478740.24723126278430.14045880956.558714876837.6271945346
23.740879612062.711493700760.3599960195614.15472047517-2.032744184043.54209286628-0.4031522750450.5424117740240.261671168217-0.8454043838250.4429958248620.744971607026-0.118492506398-0.627703784807-0.02596726351770.500797710053-0.000173334001005-0.1338347431240.541297141617-0.04743535299380.4057368180817.244245477939.965363835926.0531551883
31.374857792780.789389395084-2.092214531431.99178472238-1.220033598744.007768824190.171689594839-0.1667134247320.004995050969090.369882810638-0.0516900400184-0.252700482095-0.3828877041440.0804216969083-0.04222501616080.3939513065810.0560841573995-0.09787284831740.30379131425-0.05157816506890.37522675966424.541127599738.113771125851.3528648114
43.029768820260.900170077619-1.263576908571.76563722385-0.57384537292.853051091620.0339284960170.0771974947412-0.1256311066480.04148011629210.06396677970310.0751382077836-0.0903151295742-0.486632923381-0.0785143114450.3035200488410.0710913056384-0.06134746546930.307668150909-0.02157374915820.2702985807814.733841890332.906567676748.0877254924
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 137 )11 - 13711 - 137
22chain 'A' and (resid 138 through 226 )138 - 226138 - 199
33chain 'A' and (resid 227 through 287 )227 - 287200 - 260
44chain 'A' and (resid 288 through 456 )288 - 456261 - 429

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