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- PDB-9uce: Crystal structure of glycosyltransferase UGT73K1 in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 9uce
TitleCrystal structure of glycosyltransferase UGT73K1 in complex with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glycosyltransferase / UDP
Function / homologyUDP-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 speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhu, J.S. / Zhang, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of glycosyltransferase UGT73K1 in complex with UDP
Authors: Zhu, J.S. / Zhang, Y.
History
DepositionApr 4, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 23, 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: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4439
Polymers57,5491
Non-polymers8958
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-19 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.500, 91.500, 167.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw

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Components

#1: Protein Glycosyltransferase


Mass: 57548.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: 11431381, MTR_4g031800, MtrunA17_Chr4g0014061 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5IFH8, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 3.04 Å3/Da / Density % sol: 59.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: sodium citrate, K/Na tartrate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 22, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 36792 / % possible obs: 100 % / Redundancy: 24.67 % / CC1/2: 0.998 / Net I/σ(I): 15.51
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 24.41 % / Mean I/σ(I) obs: 3.95 / Num. unique obs: 5809 / CC1/2: 0.962 / Rrim(I) all: 0.753 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJun 30, 2024data reduction
PHENIX1.20.1-4487phasing
XDSJun 30, 2024data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.12 Å / SU ML: 0.1718 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.238
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2077 1838 5 %
Rwork0.1834 34931 -
obs0.1846 36769 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 48 150 3745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373677
X-RAY DIFFRACTIONf_angle_d0.58634990
X-RAY DIFFRACTIONf_chiral_restr0.0442547
X-RAY DIFFRACTIONf_plane_restr0.0044633
X-RAY DIFFRACTIONf_dihedral_angle_d14.90471335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.23651370.20472608X-RAY DIFFRACTION99.89
2.26-2.330.23041390.20212650X-RAY DIFFRACTION100
2.33-2.40.24541400.19652658X-RAY DIFFRACTION99.96
2.4-2.490.24261380.2072625X-RAY DIFFRACTION99.96
2.49-2.590.24311400.20062653X-RAY DIFFRACTION100
2.59-2.70.2491400.19632649X-RAY DIFFRACTION99.96
2.7-2.850.21371400.1922661X-RAY DIFFRACTION100
2.85-3.020.23491400.19842668X-RAY DIFFRACTION100
3.03-3.260.22421410.19692680X-RAY DIFFRACTION100
3.26-3.590.22641420.17842702X-RAY DIFFRACTION100
3.59-4.10.17831420.16152699X-RAY DIFFRACTION100
4.11-5.170.17691460.15732769X-RAY DIFFRACTION100
5.17-44.120.19271530.19542909X-RAY DIFFRACTION99.8
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)
10.795053520745-0.170719574451-0.009150140351150.5004890647430.08525501568340.2348696472820.009578252804990.08625552932990.0439796695664-0.2507491238830.07711539040620.105355711604-0.0842490860425-0.07844026972913.00439758956E-90.264416416946-0.0166358618251-0.03842189844540.275372919850.05720825621330.26665948804-35.51680806710.9489975791-36.3737992055
20.337133563747-0.2665003294240.2472771104561.469721069550.5010579247091.0320164782-0.0509789978176-0.3468972477260.04822799827620.6564802989410.199752341278-0.05705235763660.170476824874-0.001542327836270.006489779517990.4129783019270.00275260505097-0.02110285718420.386836769909-0.02811321290540.26579521367-16.459969778923.5945952221-10.8610750412
30.9331593844510.4416621980040.1895530481331.408416625160.3224455166031.0490873537-0.0201413720472-0.1369757087360.124147670467-0.09998364704930.0888523678205-0.0992285923455-0.04936535393140.007681609687970.0002435273090080.2412255067010.002482253428820.01211473604080.2277593274050.01927974955470.216787482532-23.656235880117.5372106899-28.5124217515
40.86530102427-0.0760820554208-0.01589010328521.53400551357-0.2071965368981.3688059681-0.125412176674-0.0928596857296-0.08941252430420.01932397203950.209704686470.2344704499070.113277069564-0.1909381256941.53266390196E-70.2227511484840.00671182129669-0.005275794847980.2564830288390.07007851413890.268636561151-39.40495228644.66569444317-24.6859717222
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 195 through 261 )195 - 261189 - 238
22chain 'A' and (resid 262 through 361 )262 - 361239 - 338
33chain 'A' and (resid 362 through 476 )362 - 476339 - 453
44chain 'A' and (resid 7 through 194 )7 - 1941 - 188

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