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- PDB-7q3s: Crystal structure of UGT706F8 from Zea mays -

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Basic information

Entry
Database: PDB / ID: 7q3s
TitleCrystal structure of UGT706F8 from Zea mays
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / UGT / silibinin / glycosyltransferase
Function / homology
Function and homology information


UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function
: / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsFredslund, F. / Bidart, G.N. / Welner, D.H.
Funding support Denmark, 3items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF18OC0034744 Denmark
Novo Nordisk FoundationNNF10CC1016517 Denmark
Danish Agency for Science Technology and Innovation7129-00003B Denmark
CitationJournal: Acs Sustain Chem Eng / Year: 2022
Title: Family 1 Glycosyltransferase UGT706F8 from Zea mays Selectively Catalyzes the Synthesis of Silibinin 7- O -beta-d-Glucoside.
Authors: Bidart, G.N. / Putkaradze, N. / Fredslund, F. / Kjeldsen, C. / Ruiz, A.G. / Duus, J.O. / Teze, D. / Welner, D.H.
History
DepositionOct 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6272
Polymers53,2231
Non-polymers4041
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-9 kcal/mol
Surface area18620 Å2
Unit cell
Length a, b, c (Å)50.188, 64.874, 76.502
Angle α, β, γ (deg.)90.000, 93.789, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycosyltransferase


Mass: 53222.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Gene: 100193773, ZEAMMB73_Zm00001d047504 / Production host: Escherichia coli (E. coli)
References: UniProt: B4FG90, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: PEG 6000 (20%), Tris 100mM, NaCl 200mM, pH 8.1 12 mg/ml 2:1 drops

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryojet / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 13, 2019 / Details: KB-mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→43.2 Å / Num. obs: 62014 / % possible obs: 94.89 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 24.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.0623 / Rpim(I) all: 0.02555 / Net I/σ(I): 17.56
Reflection shellResolution: 1.6→1.65 Å / Redundancy: 1.4 % / Rmerge(I) obs: 1.001 / Num. unique obs: 4725 / CC1/2: 0.631 / CC star: 0.88 / Rpim(I) all: 0.4238 / % possible all: 72.97

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NLM

5nlm


Resolution: 1.59→43.2 Å / SU ML: 0.2072 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6419
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1879 2098 3.38 %
Rwork0.167 59898 -
obs0.1678 61996 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.59→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 25 415 3941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01723688
X-RAY DIFFRACTIONf_angle_d1.54635035
X-RAY DIFFRACTIONf_chiral_restr0.0793566
X-RAY DIFFRACTIONf_plane_restr0.0113660
X-RAY DIFFRACTIONf_dihedral_angle_d11.22012215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.630.3368970.29652785X-RAY DIFFRACTION66.99
1.63-1.670.28481330.28793790X-RAY DIFFRACTION89.18
1.67-1.720.26491410.2674014X-RAY DIFFRACTION97.08
1.72-1.770.29891420.24964058X-RAY DIFFRACTION96.75
1.77-1.830.24421420.23434047X-RAY DIFFRACTION96.72
1.83-1.890.26381430.21834062X-RAY DIFFRACTION97
1.89-1.970.21981420.20824057X-RAY DIFFRACTION96.71
1.97-2.060.22371420.19364078X-RAY DIFFRACTION96.9
2.06-2.160.191440.17124105X-RAY DIFFRACTION97.52
2.16-2.30.19361420.16044095X-RAY DIFFRACTION97.83
2.3-2.480.18961450.15774129X-RAY DIFFRACTION97.92
2.48-2.730.1911440.15864120X-RAY DIFFRACTION97.89
2.73-3.120.17451460.15694143X-RAY DIFFRACTION98.35
3.12-3.930.16991470.1444204X-RAY DIFFRACTION98.71
3.93-43.20.15391480.14544211X-RAY DIFFRACTION97.54
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.49839062496-0.843596433834-0.1213374621661.536174461460.115788071110.948018417829-0.04679464404280.161018195714-0.262219516079-0.104060009037-0.06122041404870.6727388014940.124451628755-0.08183141783860.06712673120340.161137738587-0.0110415024699-0.03419438733820.215880301096-0.01137129355930.344378074583-18.398492493-11.5764650185-17.8943307981
20.765125809462-0.0679782866968-0.1969231904612.569102143990.3552622378140.787805306083-0.0341872227249-0.1516090966530.02966684821550.2920333676530.06837667435940.199999181966-0.0362863258878-0.0268453973027-0.02293097868910.1439687251920.0167233388259-0.005169176167120.185188626309-0.000766666225670.13616909473-6.627681222170.219844078561-9.3510940646
30.570043803880.178045938601-0.3086495144992.23035667745-0.3979597252231.57289553113-0.01564419238870.04032080624950.0442123675898-0.3811111306420.0741970062804-0.0905667620652-0.123122585561-0.00380636195079-0.03971786382110.178699296105-0.00671883725073-0.0001162258576470.140520938735-0.01260624179920.1214371026961.50277156517.08311219336-27.0049645617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 280 )
3X-RAY DIFFRACTION3chain 'A' and (resid 281 through 479 )

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