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- PDB-8gkn: Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with S... -

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Basic information

Entry
Database: PDB / ID: 8gkn
TitleCrystal structure of TuUGT202A2 (Tetur22g00270) in complex with S-naringenin
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 / NARINGENIN / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 202A2
Function and homology information
Biological speciesTetranychus urticae (two-spotted spider mite)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 S-naringenin
Authors: Arriaza, R.H. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.
History
DepositionMar 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: 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
B: UDP-glycosyltransferase 202A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2546
Polymers97,9012
Non-polymers1,3534
Water2,378132
1
A: UDP-glycosyltransferase 202A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6273
Polymers48,9511
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glycosyltransferase 202A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6273
Polymers48,9511
Non-polymers6762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.728, 167.566, 63.108
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 11 - 437 / Label seq-ID: 11 - 437

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein UDP-glycosyltransferase 202A2


Mass: 48950.504 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-NAR / NARINGENIN


Mass: 272.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.42 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein incubated with 1mM UDP- 5 mM naringenin, 0.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 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: Mar 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 26941 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / CC1/2: 0.996 / CC star: 0.999 / Rpim(I) all: 0.055 / Rrim(I) all: 0.149 / Net I/σ(I): 17.2
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1348 / CC1/2: 0.73 / CC star: 0.919 / Rpim(I) all: 0.43 / Rrim(I) all: 1.133 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
SERGUIdata collection
HKL-3000data reduction
MOLREPphasing
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→35.751 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.908 / SU B: 27.851 / SU ML: 0.282 / Cross valid method: FREE R-VALUE / ESU R Free: 0.344
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2416 1289 4.801 %
Rwork0.1781 25558 -
all0.181 --
obs-26847 99.699 %
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: 56.351 Å2
Baniso -1Baniso -2Baniso -3
1--1.177 Å2-0 Å2-0 Å2
2--0.041 Å2-0 Å2
3---1.136 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.751 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6623 0 90 132 6845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0126876
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166542
X-RAY DIFFRACTIONr_angle_refined_deg1.3511.6439344
X-RAY DIFFRACTIONr_angle_other_deg0.7191.56615119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3675852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.956529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.455101141
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.31810277
X-RAY DIFFRACTIONr_chiral_restr0.0620.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027799
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021453
X-RAY DIFFRACTIONr_nbd_refined0.2210.21385
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.25844
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23424
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23527
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0140.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1250.27
X-RAY DIFFRACTIONr_nbd_other0.2250.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0670.22
X-RAY DIFFRACTIONr_mcbond_it2.7432.9583414
X-RAY DIFFRACTIONr_mcbond_other2.7372.9583414
X-RAY DIFFRACTIONr_mcangle_it4.4415.3134264
X-RAY DIFFRACTIONr_mcangle_other4.4415.3134265
X-RAY DIFFRACTIONr_scbond_it3.5163.3183462
X-RAY DIFFRACTIONr_scbond_other3.5153.3193463
X-RAY DIFFRACTIONr_scangle_it5.7665.9415080
X-RAY DIFFRACTIONr_scangle_other5.7665.9425081
X-RAY DIFFRACTIONr_lrange_it9.20835.26928424
X-RAY DIFFRACTIONr_lrange_other9.2135.25128384
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.0513142
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.094480.05009
12AX-RAY DIFFRACTIONLocal ncs0.094480.05009
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
2.7-2.770.316930.31418190.31419460.9310.9598.25280.282
2.77-2.8450.328880.26418220.26719100.9430.9611000.232
2.845-2.9270.327870.23217470.23718360.9320.96699.89110.199
2.927-3.0170.235900.20217030.20417950.9630.97399.88860.174
3.017-3.1150.295800.19316590.19817400.940.97599.94250.161
3.115-3.2230.236840.216210.20217080.9670.97399.82440.177
3.223-3.3440.234730.19715530.19916260.9660.9761000.173
3.344-3.4790.283850.19414800.19915650.9450.9771000.175
3.479-3.6320.266830.18114270.18615100.960.981000.165
3.632-3.8080.289680.16913840.17414530.9520.98399.93120.158
3.808-4.0110.191630.16213260.16413900.9740.98599.92810.152
4.011-4.2510.263570.14312590.14813160.9590.9871000.136
4.251-4.540.202600.13411750.13612370.9730.98999.83830.129
4.54-4.8970.19520.13211070.13411620.980.98999.74180.13
4.897-5.3540.206600.14810130.15110730.9740.9871000.148
5.354-5.970.272540.1779390.1829930.9580.9821000.173
5.97-6.8610.257400.1888390.1918800.9630.9899.88640.188
6.861-8.3270.219310.1647170.1667480.9620.9831000.177
8.327-11.4690.133300.1445780.1436170.9870.98898.54130.162
11.469-35.7510.224110.2413890.2414010.9720.95999.75060.265
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)
11.05-0.6518-0.04561.70880.5732.2531-0.2145-0.1540.13820.07020.18550.35890.2112-0.06320.0290.0730.0193-0.07270.09380.04890.5212-24.642-12.311-21.941
23.079-0.4351-0.66261.6041-0.23421.83850.0028-0.0020.2966-0.07590.17230.4478-0.0802-0.0604-0.1750.02360.001-0.07260.02430.03680.627-32.718-3.159-25.725
31.4128-0.1874-0.41612.06840.07341.2531-0.01730.11150.183-0.44990.050.10450.09190.048-0.03260.1149-0.0151-0.05160.02160.04640.2984-12.486-8.446-37.882
41.5276-1.319-0.62414.1973-0.43582.255-0.1244-0.0592-0.2477-0.0213-0.0458-0.10070.32370.03990.17020.12420.03870.04180.01880.02070.30350.562-38.084-25.401
51.7534-1.2953-0.62833.55040.86072.6098-0.2443-0.2978-0.24510.21640.3024-0.50570.60830.355-0.05820.27940.20620.03660.17270.05180.644710.027-45.961-21.31
62.0668-0.9725-1.42633.31051.71312.26-0.1625-0.45340.07440.55240.3607-0.47970.21020.4663-0.19830.17340.1412-0.10830.2391-0.01810.2723.538-26.91-8.124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA11 - 112
2X-RAY DIFFRACTION2ALLA113 - 256
3X-RAY DIFFRACTION3ALLA257 - 437

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