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- PDB-7va8: Crystal structure of MiCGT -

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Basic information

Entry
Database: PDB / ID: 7va8
TitleCrystal structure of MiCGT
ComponentsUDP-glycosyltransferase 13
KeywordsTRANSFERASE / Glycosyltransferase / MiCGT
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-GLUCOSE / UDP-glycosyltransferase 13
Similarity search - Component
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85003233122 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

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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)105,4944
Polymers104,3622
Non-polymers1,1332
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-20 kcal/mol
Surface area35680 Å2
Unit cell
Length a, b, c (Å)92.39, 104.68, 109.73
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: 52180.770 Da / Num. of mol.: 2
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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (v/v) PEG3350, 0.1 M Bis-Tris pH 6.5, 200 mM calcium acetate and 4% (v/v) formamide were

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→75.75 Å / Num. obs: 25435 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 55.8365701169 Å2 / CC1/2: 0.986 / Net I/σ(I): 6.6
Reflection shellResolution: 2.85→2.92 Å / Num. unique obs: 25435 / CC1/2: 0.765

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Processing

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

2vce


Resolution: 2.85003233122→75.7423239989 Å / SU ML: 0.458448182697 / Cross valid method: FREE R-VALUE / σ(F): 1.34352284604 / Phase error: 30.9580329338
RfactorNum. reflection% reflection
Rfree0.286410936012 2002 7.88282080561 %
Rwork0.26165248777 23395 -
obs0.263633226401 25397 99.5570364563 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.9155151588 Å2
Refinement stepCycle: LAST / Resolution: 2.85003233122→75.7423239989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 72 0 6689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003749910385536857
X-RAY DIFFRACTIONf_angle_d0.8851136872269392
X-RAY DIFFRACTIONf_chiral_restr0.0312649609861101
X-RAY DIFFRACTIONf_plane_restr0.003967396900221199
X-RAY DIFFRACTIONf_dihedral_angle_d17.4044714072331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8501-2.92130.3932340939621380.3441961649441646X-RAY DIFFRACTION99.6648044693
2.9213-3.00030.3933455955331420.3354017888311638X-RAY DIFFRACTION99.7198879552
3.0003-3.08860.3630955604981460.344066268951653X-RAY DIFFRACTION99.888950583
3.0886-3.18830.3630779532981360.3203099012651658X-RAY DIFFRACTION99.9442896936
3.1883-3.30220.394796085731440.3096300030711640X-RAY DIFFRACTION99.8880179171
3.3022-3.43440.3246092969131380.2857151154061669X-RAY DIFFRACTION99.8342541436
3.4344-3.59080.3073849807831450.2840484648741644X-RAY DIFFRACTION99.6657381616
3.5908-3.78010.3023183549231490.2628373168691671X-RAY DIFFRACTION99.9450851181
3.7801-4.01690.2590131480951420.2454747362251659X-RAY DIFFRACTION99.5577667219
4.0169-4.3270.2518710084031430.2341795081581660X-RAY DIFFRACTION99.5582551077
4.327-4.76240.2045612295641390.2199719238011683X-RAY DIFFRACTION99.3998908893
4.7624-5.45130.3021819169191400.2421076992771688X-RAY DIFFRACTION99.5100707676
5.4513-6.86740.2764776268461510.2635536556711717X-RAY DIFFRACTION99.7863247863
6.8674-75.740.2346245878461490.2286709323641769X-RAY DIFFRACTION97.6081424936

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