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- PDB-6lf6: Crystal structure of ZmCGTa in complex with UDP -

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Basic information

Entry
Database: PDB / ID: 6lf6
TitleCrystal structure of ZmCGTa in complex with UDP
ComponentsUDP-glycosyltransferase 708A6
KeywordsTRANSFERASE / ZmCGTa / UDP / Complex
Function / homologyflavanone 7-O-beta-glucosyltransferase activity / UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 708A6
Function and homology information
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.044 Å
AuthorsGao, H.M. / Yun, C.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Dissection of the general two-step di- C -glycosylation pathway for the biosynthesis of (iso)schaftosides in higher plants.
Authors: Wang, Z.L. / Gao, H.M. / Wang, S. / Zhang, M. / Chen, K. / Zhang, Y.Q. / Wang, H.D. / Han, B.Y. / Xu, L.L. / Song, T.Q. / Yun, C.H. / Qiao, X. / Ye, M.
History
DepositionNov 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 16, 2020Group: 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 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: UDP-glycosyltransferase 708A6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1162
Polymers50,7121
Non-polymers4041
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-8 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.850, 82.696, 58.693
Angle α, β, γ (deg.)90.000, 105.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UDP-glycosyltransferase 708A6 / CGTa


Mass: 50711.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: UGT708A6 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A096SRM5, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.044→50 Å / Num. obs: 29864 / % possible obs: 99 % / Redundancy: 3.2 % / Biso Wilson estimate: 25.77 Å2 / Rpim(I) all: 0.04 / Net I/σ(I): 17.6
Reflection shellResolution: 2.05→2.09 Å / Num. unique obs: 28126 / Rpim(I) all: 0.297

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VCE

2vce


Resolution: 2.044→28.034 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2081 1418 5.04 %
Rwork0.1922 26708 -
obs0.193 28126 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.15 Å2 / Biso mean: 27.2757 Å2 / Biso min: 12.14 Å2
Refinement stepCycle: final / Resolution: 2.044→28.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 166 0 3601
Biso mean--29.66 --
Num. residues----457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0441-2.11720.274960.2385195968
2.1172-2.20190.25241220.2253229980
2.2019-2.30210.2271220.211251088
2.3021-2.42340.23321600.2087269694
2.4234-2.57510.24251560.2049283699
2.5751-2.77380.21341520.19812846100
2.7738-3.05260.22511520.19592885100
3.0526-3.49360.19941570.19492880100
3.4936-4.39890.18911640.17022863100
4.3989-28.0340.181370.18232934100

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