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- PDB-8sfw: Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with q... -

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Basic information

Entry
Database: PDB / ID: 8sfw
TitleCrystal structure of TuUGT202A2 (Tetur22g00270) in complex with quercetin
ComponentsUDP-glycosyltransferase 202A2
KeywordsTRANSFERASE / glycosylation / xenobiotic detoxification / flavonoids
Function / homology: / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / nucleotide binding / membrane / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 202A2
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsArriaza, R.H. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)#2020-67014- 31179 United States
CitationJournal: To Be Published
Title: Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with quercetin
Authors: Arriaza, R.H. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
History
DepositionApr 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glycosyltransferase 202A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6573
Polymers48,9511
Non-polymers7062
Water50428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.884, 109.420, 165.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein UDP-glycosyltransferase 202A2


Mass: 48950.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite)
Gene: 107367435, UGT202A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: T1KUK4
#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: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.13 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Quercetin dissolved in ETOH and let it evaporate on plate. Protein incubated with UDP. 0.2 M Ammonium acetate 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→40 Å / Num. obs: 10446 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / CC1/2: 0.96 / CC star: 0.99 / Rpim(I) all: 0.086 / Rrim(I) all: 0.209 / Net I/σ(I): 11.8
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 434 / CC1/2: 0.886 / CC star: 0.969 / Rpim(I) all: 0.258 / Rrim(I) all: 0.629 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→38.916 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.909 / SU B: 41.496 / SU ML: 0.359 / Cross valid method: FREE R-VALUE / ESU R Free: 0.435
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2641 491 4.725 %
Rwork0.2073 9900 -
all0.21 --
obs-10391 92.111 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.584 Å2
Baniso -1Baniso -2Baniso -3
1-1.171 Å2-0 Å20 Å2
2---0.694 Å2-0 Å2
3----0.477 Å2
Refinement stepCycle: LAST / Resolution: 2.75→38.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 47 28 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123314
X-RAY DIFFRACTIONr_bond_other_d0.0020.0163080
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.6414522
X-RAY DIFFRACTIONr_angle_other_deg1.0041.5637080
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.815511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02810492
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.48910124
X-RAY DIFFRACTIONr_chiral_restr0.1010.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023800
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02709
X-RAY DIFFRACTIONr_nbd_refined0.2210.2646
X-RAY DIFFRACTIONr_symmetry_nbd_other0.220.22721
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21653
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0370.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.25
X-RAY DIFFRACTIONr_nbd_other0.2330.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0790.24
X-RAY DIFFRACTIONr_mcbond_it4.6554.9781694
X-RAY DIFFRACTIONr_mcbond_other4.6544.9781694
X-RAY DIFFRACTIONr_mcangle_it7.1028.9622114
X-RAY DIFFRACTIONr_mcangle_other7.18.9622115
X-RAY DIFFRACTIONr_scbond_it6.6265.3111620
X-RAY DIFFRACTIONr_scbond_other6.6245.3141621
X-RAY DIFFRACTIONr_scangle_it9.9459.6222408
X-RAY DIFFRACTIONr_scangle_other9.9179.622408
X-RAY DIFFRACTIONr_lrange_it12.69349.8813574
X-RAY DIFFRACTIONr_lrange_other12.69149.9123575
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.75-2.8210.368260.3896370.3898210.8370.87280.75520.34
2.821-2.8980.454350.3656260.377830.8230.88984.41890.319
2.898-2.9810.4320.3036680.3077800.8710.92889.74360.263
2.981-3.0730.279340.2896750.2897440.9510.93395.29570.23
3.073-3.1730.295390.2496770.2527260.9430.95398.62260.204
3.173-3.2830.279390.2376770.2397230.9380.95899.03180.199
3.283-3.4060.269400.2026170.2066620.9420.97399.24470.178
3.406-3.5440.31250.2016280.2056720.9530.97297.17260.18
3.544-3.7010.247230.1795840.1816370.9580.98295.29040.159
3.701-3.8790.218240.1635530.1656000.9740.98396.16670.15
3.879-4.0870.168250.165090.165780.9840.98392.38750.148
4.087-4.3320.194220.1514770.1535500.9740.98590.72730.141
4.332-4.6270.184230.1534610.1555330.980.98490.80680.145
4.627-4.9920.242230.1584180.1624860.9610.98490.74070.158
4.992-5.4590.207130.1843980.1854450.9680.9892.35960.178
5.459-6.0890.296180.2063680.2114130.9560.97193.46250.201
6.089-7.0020.34200.2133180.2183640.9190.9792.85710.211
7.002-8.5070.291150.2092670.2133290.9550.9785.71430.212
8.507-11.7530.30750.22050.2032650.8930.97379.24530.213
11.753-38.9160.233100.271360.2681610.9740.94690.68320.304
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)
14.9871-1.17550.06681.0619-0.31093.90190.0701-0.03360.0282-0.29250.01370.0103-0.0741-0.1008-0.08380.342-0.00620.01910.05190.02910.04415.6376.517.224
21.27540.56210.76541.3640.96372.8580.1415-0.2169-0.05460.1197-0.0542-0.10950.5270.1044-0.08740.49790.03310.02230.16170.04760.028518.501-6.14328.962
30.71960.26410.31370.8570.76542.99940.0868-0.0765-0.1145-0.0658-0.09650.05480.5345-0.30320.00970.6076-0.08420.00630.05020.01580.04578.179-15.77910.974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA11 - 89
2X-RAY DIFFRACTION2ALLA90 - 259
3X-RAY DIFFRACTION3ALLA260 - 437

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