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- PDB-8hzz: GuApiGT (UGT79B74) -

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Basic information

Entry
Database: PDB / ID: 8hzz
TitleGuApiGT (UGT79B74)
Componentsapiosyltransferase
KeywordsPLANT PROTEIN / glycosyltransferase
Biological speciesGlycyrrhiza uralensis (Chinese licorice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, H.T. / Wang, Z.L. / Li, F.D. / Ye, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81891010/81891011 China
CitationJournal: Nat Commun / Year: 2023
Title: Insights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants.
Authors: Wang, H.T. / Wang, Z.L. / Chen, K. / Yao, M.J. / Zhang, M. / Wang, R.S. / Zhang, J.H. / Agren, H. / Li, F.D. / Li, J. / Qiao, X. / Ye, M.
History
DepositionJan 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: apiosyltransferase
B: apiosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,28211
Polymers101,4172
Non-polymers8659
Water4,576254
1
A: apiosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2857
Polymers50,7091
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint-35 kcal/mol
Surface area19290 Å2
MethodPISA
2
B: apiosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9974
Polymers50,7091
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-17 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.159, 128.676, 47.564
Angle α, β, γ (deg.)90.00, 91.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21B-697-

HOH

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Components

#1: Protein apiosyltransferase


Mass: 50708.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycyrrhiza uralensis (Chinese licorice)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.43 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.25, 28% w/v polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→19.66 Å / Num. obs: 48728 / % possible obs: 99.3 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 7.4
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 2332 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1refinement
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.66 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 2332 4.79 %
Rwork0.1914 --
obs0.1936 48728 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→19.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7028 0 45 254 7327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.959
X-RAY DIFFRACTIONf_dihedral_angle_d5.822957
X-RAY DIFFRACTIONf_chiral_restr0.0531112
X-RAY DIFFRACTIONf_plane_restr0.0091251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.33381510.27282740X-RAY DIFFRACTION99
2.24-2.290.31861300.262639X-RAY DIFFRACTION98
2.29-2.350.30181320.2432741X-RAY DIFFRACTION100
2.35-2.410.30251400.22622688X-RAY DIFFRACTION98
2.41-2.470.2508980.2182748X-RAY DIFFRACTION100
2.47-2.540.27111290.21422710X-RAY DIFFRACTION99
2.54-2.620.28111510.20462743X-RAY DIFFRACTION99
2.62-2.720.27221300.21312718X-RAY DIFFRACTION99
2.72-2.830.2721430.21262720X-RAY DIFFRACTION99
2.83-2.960.27331260.21872740X-RAY DIFFRACTION100
2.96-3.110.26671480.21332714X-RAY DIFFRACTION100
3.11-3.30.24941510.20012709X-RAY DIFFRACTION100
3.3-3.560.25581330.19252756X-RAY DIFFRACTION100
3.56-3.910.21551340.17112754X-RAY DIFFRACTION100
3.91-4.470.1831580.15242729X-RAY DIFFRACTION100
4.47-5.610.20731300.16212765X-RAY DIFFRACTION100
5.62-19.660.18171480.16552782X-RAY DIFFRACTION99

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