PDB-8sfu: Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with n...

ID or keywords:

Entry

Database: PDB / ID: 8sfu

Title

Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with naringin

Components

UDP-glycosyltransferase 202A2

Keywords

TRANSFERASE / glycosylation / xenobiotic detoxification / flavonoids

Function / homology

: / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / nucleotide binding / membrane / URIDINE-5'-DIPHOSPHATE / Chem-ZWN / UDP-glycosyltransferase 202A2

Function and homology information

Biological species

Tetranychus urticae (two-spotted spider mite)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Arriaza, R.H. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with naringin
Authors: Arriaza, R.H. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.

History

Deposition	Apr 11, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 13, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sfu.cif.gz	449.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8sfu.ent.gz	283.1 KB	Display	PDB format
PDBx/mmJSON format	8sfu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8sfu_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	8sfu_full_validation.pdf.gz	1.7 MB	Display
Data in XML	8sfu_validation.xml.gz	36.5 KB	Display
Data in CIF	8sfu_validation.cif.gz	54.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sf/8sfu ftp://data.pdbj.org/pub/pdb/validation_reports/sf/8sfu	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: UDP-glycosyltransferase 202A2

B: UDP-glycosyltransferase 202A2

hetero molecules

99.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: UDP-glycosyltransferase 202A2

hetero molecules

defined by author
Evidence: gel filtration
49.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: UDP-glycosyltransferase 202A2

hetero molecules

defined by author
49.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	47.482, 115.677, 165.693
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

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)

#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-ZWN / (2S)-5-hydroxy-2-(4-hydroxyphenyl)-4-oxo-3,4-dihydro-2H-1-benzopyran-7-yl 2-O-(6-deoxy-alpha-L-mannopyranosyl)-beta-D-glucopyranoside / Naringin Mass: 580.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₂O₁₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein incubated with 1mM UDP and 2.5 mM naringin 0.2 M Sodium Chloride 0.1 M BIS-TRIS pH 6.5 25% w/v Polyethylene glycol 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→40 Å / Num. obs: 83547 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / CC_1/2: 0.992 / CC star: 0.998 / R_pim(I) all: 0.035 / R_rim(I) all: 0.093 / Net I/σ(I): 27.7
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4097 / CC_1/2: 0.894 / CC star: 0.972 / R_pim(I) all: 0.301 / R_rim(I) all: 0.843 / % possible all: 96.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing
SERGUI		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→34.402 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.953 / WR_factor R_free: 0.22 / WR_factor R_work: 0.182 / SU B: 5.373 / SU ML: 0.087 / Average fsc free: 0.9674 / Average fsc work: 0.9767 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2138	4170	5 %
R_work	0.18	79231	-
all	0.182	-	-
obs	-	83401	97.403 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 33.838 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.042 Å²	0 Å²	-0 Å²
2-	-	1.448 Å²	0 Å²
3-	-	-	-1.406 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→34.402 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6549	0	132	609	7290

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.012	6847
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	6543
X-RAY DIFFRACTION	r_angle_refined_deg	1.671	1.645	9300
X-RAY DIFFRACTION	r_angle_other_deg	0.864	1.568	15132
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.09	5	835
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.95	5.625	32
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.161	10	1141
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.675	10	277
X-RAY DIFFRACTION	r_chiral_restr	0.084	0.2	1053
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	7701
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	1451
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	1345
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	5760
X-RAY DIFFRACTION	r_nbtor_refined	0.174	0.2	3368
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.073	0.2	3300
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.151	0.2	459
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.271	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.27	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.093	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	1.786	2.267	3352
X-RAY DIFFRACTION	r_mcbond_other	1.786	2.267	3352
X-RAY DIFFRACTION	r_mcangle_it	2.63	4.082	4183
X-RAY DIFFRACTION	r_mcangle_other	2.631	4.082	4184
X-RAY DIFFRACTION	r_scbond_it	2.587	2.634	3495
X-RAY DIFFRACTION	r_scbond_other	2.586	2.634	3496
X-RAY DIFFRACTION	r_scangle_it	4.007	4.706	5117
X-RAY DIFFRACTION	r_scangle_other	4.007	4.706	5118
X-RAY DIFFRACTION	r_lrange_it	6.124	28.65	28960
X-RAY DIFFRACTION	r_lrange_other	6.061	28.217	28428
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.095	0.05	13071

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.09496	0.05007
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09496	0.05007

LS refinement shell

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

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.8-1.847	0.286	285	0.264	5766	0.265	6218	0.948	0.955	97.3142	0.248
1.847-1.897	0.269	334	0.231	5649	0.233	6119	0.953	0.965	97.7774	0.21
1.897-1.952	0.234	272	0.204	5581	0.205	5873	0.961	0.972	99.6595	0.18
1.952-2.012	0.22	290	0.189	5362	0.191	5740	0.965	0.976	98.4669	0.165
2.012-2.078	0.212	282	0.181	5268	0.182	5612	0.971	0.979	98.8952	0.159
2.078-2.15	0.219	242	0.18	5133	0.182	5397	0.97	0.979	99.5924	0.159
2.15-2.231	0.204	236	0.177	4822	0.178	5215	0.974	0.98	96.9895	0.156
2.231-2.322	0.215	246	0.168	4699	0.17	4997	0.97	0.982	98.9594	0.149
2.322-2.424	0.22	249	0.171	4556	0.174	4841	0.97	0.981	99.2564	0.154
2.424-2.542	0.213	242	0.176	4358	0.178	4632	0.968	0.981	99.3092	0.162
2.542-2.679	0.198	215	0.178	4147	0.179	4412	0.975	0.98	98.8667	0.167
2.679-2.84	0.237	196	0.177	3968	0.18	4204	0.966	0.98	99.0485	0.17
2.84-3.035	0.231	217	0.189	3653	0.191	3924	0.965	0.977	98.6239	0.187
3.035-3.276	0.222	177	0.19	3318	0.192	3695	0.97	0.978	94.5873	0.194
3.276-3.585	0.215	155	0.176	3169	0.177	3415	0.973	0.982	97.3353	0.184
3.585-4.003	0.188	158	0.172	2705	0.173	3119	0.979	0.983	91.7922	0.186
4.003-4.612	0.19	124	0.155	2333	0.156	2760	0.98	0.986	89.0217	0.176
4.612-5.623	0.203	105	0.172	2042	0.174	2362	0.978	0.985	90.8975	0.203
5.623-7.848	0.243	91	0.19	1620	0.193	1894	0.976	0.98	90.3379	0.22
7.848-34.402	0.184	54	0.18	1065	0.18	1157	0.978	0.979	96.7156	0.228

Refinement TLS params.

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

ID	L11 (°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)
1	1.665	-0.2254	-0.0008	0.7385	0.4756	1.8649	0.0814	-0.012	-0.057	-0.1817	-0.0687	0.0155	0.0964	0.1597	-0.0127	0.2121	0.0404	-0.0038	0.0402	0.0153	0.0634	22.207	-8.2	16.994
2	0.5638	0.0698	-0.033	0.8231	-0.4673	0.9189	0.0508	-0.0899	-0.0291	0.0652	-0.0448	0.0349	-0.0297	0.013	-0.006	0.1588	-0.0127	-0.0015	0.0549	0.0236	0.0147	14.751	6.225	27.534
3	0.9727	0.1137	-0.0801	0.4454	-0.3287	1.2289	-0.0043	-0.0625	-0.0615	0.0135	-0.0263	-0.0321	0.0001	0.0461	0.0306	0.1437	-0.0097	-0.0091	0.0065	0.0083	0.0318	23.017	20.011	7.13
4	1.9737	2.0711	-0.0194	10.1045	-4.6167	2.6664	-0.0027	0.0989	-0.2239	0.1711	-0.1836	-0.5468	-0.0872	0.1762	0.1863	0.0797	0.032	0.0078	0.125	0.0379	0.0507	35.814	1.612	28.766
5	1.8665	0.6915	0.8767	1.296	0.7063	2.8936	-0.0512	0.116	-0.2059	0.0179	0.1516	-0.1043	-0.133	0.0874	-0.1003	0.1789	-0.0177	0.0328	0.0575	-0.0619	0.0785	19.921	9.937	-18.952
6	0.7497	-0.0798	0.3306	0.5377	-0.3281	1.5947	0.1033	0.0807	-0.191	-0.1476	-0.0103	0.0331	0.1647	-0.0506	-0.093	0.1809	-0.0122	-0.0136	0.0643	-0.0684	0.0953	15.078	-5.577	-30.063
7	1.3781	-0.2633	0.0786	0.4705	-0.2832	2.8668	-0.0129	-0.0193	-0.2676	0.0359	0.0509	0.0225	0.3262	0.181	-0.038	0.2306	0.036	-0.0136	0.0245	-0.019	0.1715	28.738	-16.134	-10.446
8	5.4449	-5.1886	2.7827	9.3002	0.9042	8.4096	0.3383	0.025	0.3074	-0.7664	0.4789	-1.0547	-0.4038	1.1734	-0.8172	0.1157	-0.1187	0.1327	0.2472	-0.1824	0.2	31.79	10.259	-34.621

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	11 - 81
2	X-RAY DIFFRACTION	2	ALL	A	82 - 260
3	X-RAY DIFFRACTION	3	ALL	A	261 - 409
4	X-RAY DIFFRACTION	4	ALL	A	410 - 437

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