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- PDB-8inv: Crystal structure of UGT74AN3-UDP-BUF -

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Basic information

Entry
Database: PDB / ID: 8inv
TitleCrystal structure of UGT74AN3-UDP-BUF
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / COMPLEX
Function / homology
Function and homology information


UDP-glycosyltransferase activity / hexosyltransferase 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
bufalin / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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)53,4564
Polymers52,5431
Non-polymers9133
Water4,143230
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 area17370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.682, 52.281, 200.852
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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine 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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-BUF / bufalin / Bufalin


Mass: 386.524 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H34O4 / Comment: toxin*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
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: Oct 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→19.76 Å / Num. obs: 42800 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 26.01 Å2 / CC1/2: 0.989 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 2584 / CC1/2: 0.961

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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: 1.85→19.76 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 2160 5.13 %
Rwork0.1838 --
obs0.1854 42107 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 61 230 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073546
X-RAY DIFFRACTIONf_angle_d0.9464817
X-RAY DIFFRACTIONf_dihedral_angle_d7.22476
X-RAY DIFFRACTIONf_chiral_restr0.058557
X-RAY DIFFRACTIONf_plane_restr0.007594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.28171290.21672640X-RAY DIFFRACTION100
1.89-1.940.28971530.22892602X-RAY DIFFRACTION100
1.94-1.990.25031110.20172661X-RAY DIFFRACTION100
1.99-2.050.26371270.18892615X-RAY DIFFRACTION100
2.05-2.120.23161460.18812616X-RAY DIFFRACTION100
2.12-2.190.22251410.17662654X-RAY DIFFRACTION100
2.19-2.280.23221300.18872654X-RAY DIFFRACTION100
2.28-2.380.20571570.19012629X-RAY DIFFRACTION100
2.38-2.510.25151470.18762617X-RAY DIFFRACTION100
2.51-2.670.22861590.19482643X-RAY DIFFRACTION100
2.67-2.870.23961420.19092673X-RAY DIFFRACTION100
2.87-3.160.22811510.19852653X-RAY DIFFRACTION100
3.16-3.610.21141660.17942677X-RAY DIFFRACTION100
3.61-4.540.17951520.15782747X-RAY DIFFRACTION100
4.55-19.760.18951490.18192866X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.9524 Å / Origin y: 21.093 Å / Origin z: 75.4072 Å
111213212223313233
T0.1345 Å20.0036 Å20.0296 Å2-0.1494 Å2-0.0454 Å2--0.1897 Å2
L1.9297 °2-0.2643 °2-0.6607 °2-1.0942 °20.4484 °2--2.4341 °2
S0.0428 Å °-0.3345 Å °0.2743 Å °-0.0436 Å °0.0255 Å °-0.0418 Å °-0.1789 Å °0.0095 Å °-0.0162 Å °
Refinement TLS groupSelection details: all

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