PDB-8sft: Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with k...

ID or keywords:

Entry

Database: PDB / ID: 8sft

Title

Crystal structure of TuUGT202A2 (Tetur22g00270) in complex with kaempferol

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 /

membrane / Chem-KMP / URIDINE-5'-DIPHOSPHATE / Unknown ligand / UDP-glycosyltransferase 202A2

Function and homology information

Biological species

Tetranychus urticae (two-spotted spider mite)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 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 kaempferol
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	Apr 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8sft.cif.gz	860.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8sft.ent.gz	548.7 KB	Display	PDB format
PDBx/mmJSON format	8sft.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sf/8sft ftp://data.pdbj.org/pub/pdb/validation_reports/sf/8sft	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) #137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: UDP-glycosyltransferase 202A2

B: UDP-glycosyltransferase 202A2

C: UDP-glycosyltransferase 202A2

D: UDP-glycosyltransferase 202A2

hetero molecules

200 kDa, 4 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
50.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: UDP-glycosyltransferase 202A2

hetero molecules

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

3

C: UDP-glycosyltransferase 202A2

hetero molecules

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

4

D: UDP-glycosyltransferase 202A2

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.277, 159.906, 163.311
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
3	2	A
4	2	A
5	3	A
6	3	A
7	4	A
8	4	A
9	5	A
10	5	A
11	6	A
12	6	A

NCS domain segments:

Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth seq-ID	Label seq-ID
1	1	1	LYS	LYS	11 - 436	11 - 436
2	1	1	LYS	LYS	11 - 436	11 - 436
3	2	2	LEU	LEU	11 - 437	11 - 437
4	2	2	LEU	LEU	11 - 437	11 - 437
5	3	3	LEU	LEU	11 - 437	11 - 437
6	3	3	LEU	LEU	11 - 437	11 - 437
7	4	4	LYS	LYS	11 - 436	11 - 436
8	4	4	LYS	LYS	11 - 436	11 - 436
9	5	5	LEU	LEU	11 - 437	11 - 437
10	5	5	LEU	LEU	11 - 437	11 - 437
11	6	6	LEU	LEU	11 - 437	11 - 437
12	6	6	LEU	LEU	11 - 437	11 - 437

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules ABCD

#1: Protein	UDP-glycosyltransferase 202A2 Mass: 48950.504 Da / Num. of mol.: 4 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

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Non-polymers , 5 types, 216 molecules

#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical	ChemComp-KMP / 3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE / KAEMPHEROL / Kaempferol Mass: 286.236 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₅H₁₀O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-UNL / UNKNOWN LIGAND Mass: 103.120 Da / Num. of mol.: 13 / Source method: obtained synthetically / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.78 Å³/Da / Density % sol: 55.7 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein incubated with 1 mM UDP and kaempferol dissolved in ethanol. 0.2 M Ammonium sulfate 0.1 M HEPES pH 7.5 25% PEG 3350

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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: Mar 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: 2.75→40 Å / Num. obs: 56602 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / CC_1/2: 0.985 / CC star: 0.996 / R_pim(I) all: 0.072 / R_rim(I) all: 0.183 / Net I/σ(I): 14
Reflection shell	Resolution: 2.75→2.82 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2850 / CC_1/2: 0.829 / CC star: 0.952 / R_pim(I) all: 0.313 / R_rim(I) all: 0.846 / % possible all: 98.4

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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: 2.75→39.588 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.912 / SU B: 25.205 / SU ML: 0.255 / Cross valid method: FREE R-VALUE / ESU R Free: 0.336
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2316	2773	5.046 %
R_work	0.1915	52178	-
all	0.193	-	-
obs	-	54951	95.592 %

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: 71.855 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.468 Å²	-0 Å²	0 Å²
2-	-	-0.83 Å²	-0 Å²
3-	-	-	-0.638 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→39.588 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13198	0	186	194	13578

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.012	13689
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.016	13033
X-RAY DIFFRACTION	r_angle_refined_deg	1.518	1.644	18588
X-RAY DIFFRACTION	r_angle_other_deg	0.823	1.569	30115
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.711	5	1691
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	3.262	5	57
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.562	10	2311
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	17.075	10	558
X-RAY DIFFRACTION	r_chiral_restr	0.063	0.2	2086
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	15551
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	2920
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	2588
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.217	0.2	11050
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	6587
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.07	0.2	6540
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.149	0.2	275
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.137	0.2	10
X-RAY DIFFRACTION	r_nbd_other	0.21	0.2	68
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.167	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	5.226	5.535	6785
X-RAY DIFFRACTION	r_mcbond_other	5.226	5.534	6785
X-RAY DIFFRACTION	r_mcangle_it	7.718	10.014	8469
X-RAY DIFFRACTION	r_mcangle_other	7.718	10.015	8470
X-RAY DIFFRACTION	r_scbond_it	5.785	6.017	6904
X-RAY DIFFRACTION	r_scbond_other	5.785	6.016	6897
X-RAY DIFFRACTION	r_scangle_it	8.724	10.864	10119
X-RAY DIFFRACTION	r_scangle_other	8.724	10.864	10120
X-RAY DIFFRACTION	r_lrange_it	13.131	66.401	56146
X-RAY DIFFRACTION	r_lrange_other	13.134	66.409	56097
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.093	0.05	13301
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.089	0.05	13230
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.091	0.05	12679
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.089	0.05	13255
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.092	0.05	12764
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.082	0.05	12672

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	0.09309	0.05008
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09309	0.05008
2	3	A	X-RAY DIFFRACTION	Local ncs	0.08904	0.05008
2	4	A	X-RAY DIFFRACTION	Local ncs	0.08904	0.05008
3	5	A	X-RAY DIFFRACTION	Local ncs	0.0913	0.05008
3	6	A	X-RAY DIFFRACTION	Local ncs	0.0913	0.05008
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08948	0.05008
4	8	A	X-RAY DIFFRACTION	Local ncs	0.08948	0.05008
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09212	0.05008
5	10	A	X-RAY DIFFRACTION	Local ncs	0.09212	0.05008
6	11	A	X-RAY DIFFRACTION	Local ncs	0.08199	0.05008
6	12	A	X-RAY DIFFRACTION	Local ncs	0.08199	0.05008

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
2.75-2.821	0.351	210	0.284	3904	0.288	4181	0.931	0.947	98.3975	0.258
2.821-2.898	0.308	191	0.245	3814	0.248	4063	0.941	0.961	98.5725	0.216
2.898-2.982	0.275	210	0.235	3685	0.237	3948	0.955	0.964	98.6575	0.205
2.982-3.073	0.289	178	0.221	3656	0.224	3861	0.939	0.968	99.3007	0.194
3.073-3.173	0.266	192	0.221	3469	0.223	3720	0.951	0.968	98.414	0.193
3.173-3.283	0.259	174	0.215	3422	0.217	3621	0.956	0.969	99.3096	0.19
3.283-3.407	0.263	174	0.197	3326	0.2	3503	0.956	0.976	99.9144	0.177
3.407-3.545	0.234	176	0.182	3191	0.185	3374	0.962	0.981	99.7925	0.169
3.545-3.701	0.211	148	0.178	3062	0.18	3231	0.973	0.982	99.35	0.167
3.701-3.88	0.209	151	0.173	2882	0.175	3103	0.973	0.981	97.7441	0.165
3.88-4.087	0.2	139	0.16	2739	0.162	2969	0.976	0.984	96.935	0.155
4.087-4.332	0.188	123	0.149	2510	0.151	2805	0.975	0.986	93.8681	0.148
4.332-4.628	0.173	114	0.148	2246	0.149	2645	0.981	0.986	89.225	0.148
4.628-4.993	0.174	124	0.15	2049	0.152	2477	0.981	0.986	87.7271	0.153
4.993-5.461	0.222	121	0.172	1943	0.175	2289	0.971	0.982	90.1704	0.175
5.461-6.091	0.239	93	0.182	1831	0.185	2089	0.966	0.981	92.1015	0.187
6.091-7.005	0.274	102	0.2	1590	0.204	1868	0.954	0.973	90.5782	0.207
7.005-8.513	0.206	83	0.193	1261	0.194	1595	0.968	0.976	84.2633	0.207
8.513-11.771	0.236	43	0.187	892	0.19	1285	0.972	0.982	72.7626	0.207
11.771-39.588	0.271	27	0.321	688	0.32	813	0.959	0.938	87.9459	0.351

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	0.4483	0.265	-0.3311	0.2165	-0.2715	0.8826	-0.0131	-0.0742	0.0891	-0.0304	0.0368	0.0059	0.0365	-0.0293	-0.0237	0.0197	0.0093	0.0079	0.2618	-0.0271	0.2708	31.368	5.057	67.184
2	0.2169	0.0021	-0.0757	0.5389	-0.2643	0.6457	-0.0026	0.0703	-0.0201	0.0246	0.0152	-0.0159	0.0585	-0.0178	-0.0126	0.0115	-0.0034	0.0051	0.2421	-0.0284	0.277	28.985	-9.758	28.206
3	0.4178	-0.5298	0.1577	1.2472	-0.4622	0.31	0.0384	0.1028	-0.1105	0.031	-0.0391	0.1256	-0.0181	0.0354	0.0008	0.0157	0.0102	-0.0089	0.14	-0.045	0.3965	71.478	-28.95	34.919
4	0.4321	-0.0749	-0.2389	0.7698	-0.2409	0.4662	-0.0132	-0.0554	0.1055	0.0142	0.0234	0.1067	0.0535	0.0501	-0.0102	0.0161	-0.0093	-0.0031	0.1534	-0.0276	0.3539	74.032	9.155	50.296

Refinement TLS group

Selection: ALL

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