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- PDB-8ino: Crystal structure of UGT74AN3 in complex UDP and PER -

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Basic information

Entry
Database: PDB / ID: 8ino
TitleCrystal structure of UGT74AN3 in complex UDP and PER
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
Chem-Q30 / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLong, F. / Huang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Catalysis / Year: 2024
Title: Substrate Promiscuity, Crystal Structure, and Application of a Plant UDP-Glycosyltransferase UGT74AN3
Authors: Huang, W. / Zhang, X. / Li, J. / Lv, J. / Wang, Y. / He, Y. / Song, J. / Agren, H. / Jiang, R. / Deng, Z. / Long, F.
History
DepositionMar 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: 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)53,4604
Polymers52,5431
Non-polymers9173
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.608, 52.200, 200.701
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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: 52543.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A385Z961, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-Q30 / 3-[(3S,5S,8S,9S,10R,13R,14S,17R)-10,13-dimethyl-3,5,14-tris(oxidanyl)-2,3,4,6,7,8,9,11,12,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-17-yl]-2H-furan-5-one


Mass: 390.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34O5
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG2000MME, 0.1M Hepes (7.5), 0.2M potassium nitro

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Data collection

DiffractionMean temperature: 203 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→19.83 Å / Num. obs: 22111 / % possible obs: 99.8 % / Redundancy: 25.7 % / Biso Wilson estimate: 30.58 Å2 / CC1/2: 0.995 / Net I/σ(I): 14.7
Reflection shellResolution: 2.3→2.38 Å / Num. unique obs: 2152 / CC1/2: 0.98

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Processing

Software
NameVersionClassification
Blu-Ice1.19.2_4158data collection
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.83 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 1079 4.88 %
Rwork0.1841 --
obs0.1863 22102 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3324 0 61 101 3486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083474
X-RAY DIFFRACTIONf_angle_d0.9114721
X-RAY DIFFRACTIONf_dihedral_angle_d8.809467
X-RAY DIFFRACTIONf_chiral_restr0.054547
X-RAY DIFFRACTIONf_plane_restr0.006581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.25261180.18352599X-RAY DIFFRACTION100
2.4-2.530.25431350.19292571X-RAY DIFFRACTION100
2.53-2.690.26551250.19772595X-RAY DIFFRACTION100
2.69-2.90.24091350.20852595X-RAY DIFFRACTION100
2.9-3.190.2891220.20352603X-RAY DIFFRACTION100
3.19-3.650.21111450.18592620X-RAY DIFFRACTION100
3.65-4.580.19491530.15832653X-RAY DIFFRACTION100
4.58-19.830.21791460.18282787X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -11.3656 Å / Origin y: 20.5534 Å / Origin z: 75.4261 Å
111213212223313233
T0.181 Å20.0052 Å20.0192 Å2-0.1822 Å2-0.0225 Å2--0.2244 Å2
L1.8448 °2-0.1698 °2-0.4251 °2-0.9764 °20.4376 °2--2.4597 °2
S0.0208 Å °-0.323 Å °0.2546 Å °0.0009 Å °0.0029 Å °-0.0238 Å °-0.1788 Å °-0.0136 Å °-0.0013 Å °
Refinement TLS groupSelection details: all

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