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- PDB-7vaa: Crystal structure of MiCGT(W93V/V124F/ F191A/R282H) in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7vaa
TitleCrystal structure of MiCGT(W93V/V124F/ F191A/R282H) in complex with UDPs
ComponentsUDP-glycosyltransferase 13
KeywordsTRANSFERASE / MiCGT / Glycosyltransferase
Function / homology
Function and homology information


xylosyltransferase activity / UDP-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 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 13
Similarity search - Component
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.10002756491 Å
AuthorsZhong, L. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Catalysis / Year: 2021
Title: Directed Evolution of a Plant Glycosyltransferase for Chemo- and Regioselective Glycosylation of Pharmaceutically Significant Flavonoids
Authors: Wen, Z. / Zhang, Z.M. / Zhong, L. / Fan, J. / Li, M. / Ma, Y. / Zhou, Y. / Zhang, W. / Guo, B. / Chen, B. / Wang, J.B.
History
DepositionAug 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 6, 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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glycosyltransferase 13
B: UDP-glycosyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,9014
Polymers104,0932
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-28 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.705, 103.759, 109.713
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein UDP-glycosyltransferase 13 / MiUGT13 / C-glycosyltransferase / MiCGT


Mass: 52046.586 Da / Num. of mol.: 2 / Mutation: W93V, V124F, F191A, R282H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mangifera indica (mango) / Gene: CGT, UGT13 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0M4KE44, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
Has ligand of interestY
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) PEG3350, 0.1 M Bis-Tris pH 7.0, 200 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 19961 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.0425676209 Å2 / CC1/2: 0.896 / Net I/σ(I): 8.7
Reflection shellResolution: 3.1→3.15 Å / Num. unique obs: 1362 / CC1/2: 0.739

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692+SVNrefinement
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VCE

2vce


Resolution: 3.10002756491→48.4959484106 Å / SU ML: 0.433450366629 / Cross valid method: FREE R-VALUE / σ(F): 1.36306650605 / Phase error: 30.3573503523
RfactorNum. reflection% reflection
Rfree0.2887922588 1963 10.0558373034 %
Rwork0.245149574543 17558 -
obs0.249526368324 19521 99.571537873 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.5961658641 Å2
Refinement stepCycle: LAST / Resolution: 3.10002756491→48.4959484106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6988 0 50 0 7038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002897632555177212
X-RAY DIFFRACTIONf_angle_d0.7687441611129822
X-RAY DIFFRACTIONf_chiral_restr0.027046771661116
X-RAY DIFFRACTIONf_plane_restr0.003570823780351258
X-RAY DIFFRACTIONf_dihedral_angle_d13.80987031662610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1001-3.17750.3972372646041410.3164419021741221X-RAY DIFFRACTION99.6342355523
3.1775-3.26340.4411764669751480.3116853610821229X-RAY DIFFRACTION99.8549673677
3.2634-3.35940.3341334350171310.2746233584831245X-RAY DIFFRACTION99.7824510515
3.3594-3.46780.3189479880571330.2858752862781246X-RAY DIFFRACTION99.8551774077
3.4678-3.59180.2977961246271440.2631700164041224X-RAY DIFFRACTION99.8540145985
3.5918-3.73550.2738664704591410.2578099348781241X-RAY DIFFRACTION99.9276934201
3.7355-3.90540.2470102120931340.251562319031239X-RAY DIFFRACTION99.8545454545
3.9054-4.11120.3052753388851420.2172686972531256X-RAY DIFFRACTION99.8571428571
4.1112-4.36870.2407859214841310.2269804252581252X-RAY DIFFRACTION99.6397694524
4.3687-4.70570.2720327617441460.2222781040231247X-RAY DIFFRACTION99.7851002865
4.7057-5.17880.2600000819791300.2231809006731284X-RAY DIFFRACTION99.8587570621
5.1788-5.9270.288461224991470.2399522993171257X-RAY DIFFRACTION100
5.927-7.46310.313007417541470.2618200471481290X-RAY DIFFRACTION99.7916666667
7.4631-48.490.2518772287971480.2168069996231327X-RAY DIFFRACTION96.5946299935

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