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- PDB-6jtd: Crystal structure of TcCGT1 in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 6jtd
TitleCrystal structure of TcCGT1 in complex with UDP
ComponentsC-glycosyltransferase
KeywordsTRANSFERASE / C-glycosyltransferase / glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase 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 / Glycosyltransferase
Similarity search - Component
Biological speciesTrollius chinensis (jin lian hua)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsZhao, P. / Yun, C.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: Molecular and Structural Characterization of a Promiscuous C-Glycosyltransferase from Trollius chinensis.
Authors: He, J.B. / Zhao, P. / Hu, Z.M. / Liu, S. / Kuang, Y. / Zhang, M. / Li, B. / Yun, C.H. / Qiao, X. / Ye, M.
History
DepositionApr 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C-glycosyltransferase
B: C-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,43964
Polymers107,9062
Non-polymers4,53262
Water12,160675
1
A: C-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,84726
Polymers53,9531
Non-polymers1,89425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: C-glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,59238
Polymers53,9531
Non-polymers2,63937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.304, 108.702, 90.432
Angle α, β, γ (deg.)90.00, 106.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C-glycosyltransferase / CGT1


Mass: 53953.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trollius chinensis (jin lian hua) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4Y5RXX8*PLUS
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 675 / Source method: isolated from a natural source / Formula: H2O

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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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M potassium chloride, 0.02M Tris 7.0, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 88344 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.981 / Net I/σ(I): 11.6
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / CC1/2: 0.696 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementResolution: 1.85→39.682 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.06
RfactorNum. reflection% reflection
Rfree0.1974 4424 5.01 %
Rwork0.1693 --
obs0.1707 88323 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7334 50 240 675 8299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127783
X-RAY DIFFRACTIONf_angle_d1.20510478
X-RAY DIFFRACTIONf_dihedral_angle_d17.8842875
X-RAY DIFFRACTIONf_chiral_restr0.0621195
X-RAY DIFFRACTIONf_plane_restr0.0081319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8461-1.86710.30121350.26512529X-RAY DIFFRACTION90
1.8671-1.88910.29821560.23872754X-RAY DIFFRACTION98
1.8891-1.91210.26361490.22232777X-RAY DIFFRACTION98
1.9121-1.93630.27761280.22842810X-RAY DIFFRACTION98
1.9363-1.96180.26541450.21722757X-RAY DIFFRACTION98
1.9618-1.98860.23781560.2172753X-RAY DIFFRACTION98
1.9886-2.01710.24821600.20242797X-RAY DIFFRACTION98
2.0171-2.04720.24941610.20122750X-RAY DIFFRACTION99
2.0472-2.07910.22611560.18672788X-RAY DIFFRACTION98
2.0791-2.11320.23151220.18322794X-RAY DIFFRACTION99
2.1132-2.14970.22281420.17882787X-RAY DIFFRACTION98
2.1497-2.18880.22131350.17882802X-RAY DIFFRACTION99
2.1888-2.23090.19681380.17442823X-RAY DIFFRACTION99
2.2309-2.27640.2341460.17582808X-RAY DIFFRACTION99
2.2764-2.32590.21091370.17352800X-RAY DIFFRACTION99
2.3259-2.380.21761460.17352835X-RAY DIFFRACTION99
2.38-2.43950.19481360.17062815X-RAY DIFFRACTION99
2.4395-2.50540.21211410.16852784X-RAY DIFFRACTION99
2.5054-2.57910.17871340.16312830X-RAY DIFFRACTION99
2.5791-2.66240.18661580.15532829X-RAY DIFFRACTION99
2.6624-2.75750.17221680.15682760X-RAY DIFFRACTION99
2.7575-2.86790.20331830.16482793X-RAY DIFFRACTION99
2.8679-2.99840.19531490.16222833X-RAY DIFFRACTION100
2.9984-3.15640.20361650.16762819X-RAY DIFFRACTION100
3.1564-3.3540.19071490.16272830X-RAY DIFFRACTION100
3.354-3.61290.18881510.15052822X-RAY DIFFRACTION100
3.6129-3.97610.16531400.15082857X-RAY DIFFRACTION100
3.9761-4.55080.16841180.1432875X-RAY DIFFRACTION100
4.5508-5.73070.16951660.15682835X-RAY DIFFRACTION100
5.7307-39.69090.15361540.17232853X-RAY DIFFRACTION98

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