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- PDB-8ind: Crystal structure of UGT74AN3-UDP-RES -

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Basic information

Entry
Database: PDB / ID: 8ind
TitleCrystal structure of UGT74AN3-UDP-RES
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-6JI / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsHuang, 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 9, 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)53,5854
Polymers52,6741
Non-polymers9113
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-9 kcal/mol
Surface area17540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.995, 52.911, 201.119
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: 52674.379 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-6JI / 5-[(1R,2S,4R,6R,7R,10S,11S,14S,16R)-14-hydroxy-7,11-dimethyl-3-oxapentacyclo[8.8.0.02,4.02,7.011,16]octadecan-6-yl]pyran-2-one / Resibufogenin


Mass: 384.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32O4
#3: 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
#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 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
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: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.85→19.46 Å / Num. obs: 42938 / % possible obs: 99.9 % / Redundancy: 13 % / Biso Wilson estimate: 27.11 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 2638 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
Blu-Ice1.19.2_4158data collection
XDS1.19.2_4158data reduction
Aimlessdata scaling
PHENIXmodel building
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.46 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 2143 4.99 %
Rwork0.1825 --
obs0.1842 42923 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→19.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 61 266 3701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083564
X-RAY DIFFRACTIONf_angle_d0.9994846
X-RAY DIFFRACTIONf_dihedral_angle_d8.414482
X-RAY DIFFRACTIONf_chiral_restr0.063562
X-RAY DIFFRACTIONf_plane_restr0.007599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.890.31981570.28442662X-RAY DIFFRACTION100
1.89-1.940.27861350.2282654X-RAY DIFFRACTION100
1.94-1.990.22751500.19952672X-RAY DIFFRACTION100
1.99-2.050.22991330.19022676X-RAY DIFFRACTION100
2.05-2.120.24441390.18082699X-RAY DIFFRACTION100
2.12-2.190.23071410.18672690X-RAY DIFFRACTION100
2.19-2.280.20461420.18152668X-RAY DIFFRACTION100
2.28-2.380.24121460.19092685X-RAY DIFFRACTION100
2.38-2.510.22621470.18372724X-RAY DIFFRACTION100
2.51-2.670.22411390.19162710X-RAY DIFFRACTION100
2.67-2.870.22221330.1912723X-RAY DIFFRACTION100
2.87-3.160.24361240.19072748X-RAY DIFFRACTION100
3.16-3.610.19841610.182740X-RAY DIFFRACTION100
3.61-4.540.17851460.1542799X-RAY DIFFRACTION100
4.55-19.460.20821500.17942930X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -10.5799 Å / Origin y: 21.4953 Å / Origin z: 75.6767 Å
111213212223313233
T0.1777 Å2-0.0037 Å20.0186 Å2-0.1655 Å2-0.0433 Å2--0.2128 Å2
L1.3124 °2-0.1307 °2-0.4413 °2-0.5049 °20.2313 °2--1.5614 °2
S0.0202 Å °-0.2519 Å °0.1536 Å °-0.0549 Å °0.0158 Å °-0.019 Å °-0.0241 Å °-0.0075 Å °0.0042 Å °
Refinement TLS groupSelection details: all

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