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- PDB-7w10: UGT74AN2 -

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Basic information

Entry
Database: PDB / ID: 7w10
TitleUGT74AN2
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
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 speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsWei, H. / Long, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2022
Title: Functional and Structural Dissection of a Plant Steroid 3-O-Glycosyltransferase Facilitated the Engineering Enhancement of Sugar Donor Promiscuity
Authors: Huang, W. / He, Y. / Jiang, R. / Deng, Z. / Long, F.
History
DepositionNov 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)54,8654
Polymers53,9521
Non-polymers9133
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.178, 74.640, 63.609
Angle α, β, γ (deg.)90.000, 95.572, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Glycosyltransferase / Plant steroid glycosyltransferase UGT74AN2


Mass: 53952.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calotropis gigantea (mudar) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A385Z7H9, 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 / Comment: UDP*YM
#3: 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
#4: Chemical ChemComp-BUF / bufalin


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


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, 0.1M sodium chloride, 0.1M MES (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.15→48.28 Å / Num. obs: 27058 / % possible obs: 99.4 % / Redundancy: 17.9 % / Biso Wilson estimate: 30.41 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.1
Reflection shellResolution: 2.15→2.21 Å / Num. unique obs: 2104 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L8Z

6l8z


Resolution: 2.15→42.7 Å / SU ML: 0.2724 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2453
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2245 1296 4.8 %
Rwork0.196 25693 -
obs0.1974 26989 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.22 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3381 0 61 22 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00853522
X-RAY DIFFRACTIONf_angle_d0.8624802
X-RAY DIFFRACTIONf_chiral_restr0.0512554
X-RAY DIFFRACTIONf_plane_restr0.006597
X-RAY DIFFRACTIONf_dihedral_angle_d8.2543485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.230.31991350.26222755X-RAY DIFFRACTION95.79
2.23-2.330.31431310.2452847X-RAY DIFFRACTION99.13
2.33-2.460.26161440.22162840X-RAY DIFFRACTION99.33
2.46-2.610.24661560.21672821X-RAY DIFFRACTION99.63
2.61-2.810.27941470.22342871X-RAY DIFFRACTION99.93
2.81-3.10.26121370.21342879X-RAY DIFFRACTION99.87
3.1-3.540.21921530.19142871X-RAY DIFFRACTION99.83
3.54-4.460.18531480.16612873X-RAY DIFFRACTION99.93
4.46-42.70.18441450.1742936X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: -18.7806981752 Å / Origin y: -9.96885941398 Å / Origin z: -10.7523806038 Å
111213212223313233
T0.255740890373 Å2-0.0647770270254 Å20.0227376457775 Å2-0.179372466538 Å20.00632310978897 Å2--0.184013007838 Å2
L1.26859129473 °2-0.708028631501 °20.603586845938 °2-0.756561779719 °2-0.655138765238 °2--1.52508041932 °2
S0.0071963524504 Å °0.114527773563 Å °0.0980239453309 Å °-0.011300915493 Å °-0.0631267828976 Å °-0.0493518948255 Å °-0.0795375897482 Å °0.172863667885 Å °0.0463371046233 Å °
Refinement TLS groupSelection details: all

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