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- PDB-7w11: glycosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7w11
Titleglycosyltransferase
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
DIGITOXIGENIN / alpha-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWei, H. / Feng, L.
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 19, 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)54,9114
Polymers53,9521
Non-polymers9593
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area18060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.753, 76.533, 63.210
Angle α, β, γ (deg.)90.000, 97.194, 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: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-DTX / DIGITOXIGENIN / 4-(3,14-DIHYDROXY-10,13-DIMETHYL-HEXADECAHYDRO-CYCLOPENTA[A]PHENANTHREN-17-YL)-5H-FURAN-2-ONE


Mass: 374.514 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H34O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
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: 2.45→19.79 Å / Num. obs: 17505 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.56 Å2 / CC1/2: 0.96 / Net I/σ(I): 6.7
Reflection shellResolution: 2.45→2.55 Å / Num. unique obs: 1953 / CC1/2: 0.728

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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: 2.45→19.79 Å / SU ML: 0.2899 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.2933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2442 891 5.1 %
Rwork0.1928 16576 -
obs0.1955 17467 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.07 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 63 12 3385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813456
X-RAY DIFFRACTIONf_angle_d0.9534718
X-RAY DIFFRACTIONf_chiral_restr0.0501551
X-RAY DIFFRACTIONf_plane_restr0.0071584
X-RAY DIFFRACTIONf_dihedral_angle_d9.9009484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.60.33371450.23262712X-RAY DIFFRACTION97.94
2.6-2.80.2841440.21672780X-RAY DIFFRACTION99.46
2.8-3.080.29631530.2232765X-RAY DIFFRACTION98.98
3.08-3.530.25751400.18972758X-RAY DIFFRACTION98.07
3.53-4.440.21911530.16592766X-RAY DIFFRACTION99.15
4.44-19.790.19241560.18422795X-RAY DIFFRACTION97.88
Refinement TLS params.Method: refined / Origin x: -17.3690509217 Å / Origin y: -9.17708140688 Å / Origin z: -10.2572321991 Å
111213212223313233
T0.161006267565 Å2-0.0375578572622 Å20.00744634199191 Å2-0.13335918675 Å20.00931202755843 Å2--0.15756929289 Å2
L1.13933732119 °2-0.620794347683 °20.290709985371 °2-0.844624341122 °2-0.39585617897 °2--0.799613393582 °2
S-0.055782892162 Å °0.00882511610837 Å °0.0620172597668 Å °0.0476269807 Å °0.00551176286059 Å °-0.0418457577926 Å °-0.0504965040208 Å °0.0364297108781 Å °0.0518786040341 Å °
Refinement TLS groupSelection details: all

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