PDB-7mco: Crystal Structure of Tetur04g02350

ID or keywords:

Entry

Database: PDB / ID: 7mco

Title

Crystal Structure of Tetur04g02350

Components

UDP-glycosyltransferase 203A2

Keywords

TRANSFERASE

Function / homology

UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 203A2

Function and homology information

Biological species

Tetranychus urticae (two-spotted spider mite)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Danehsian, L. / Kluza, A. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal Structure of Tetur04g02350
Authors: Danehsian, L. / Kluza, A. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M.

History

Deposition	Apr 2, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 27, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mco.cif.gz	346.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7mco.ent.gz	269 KB	Display	PDB format
PDBx/mmJSON format	7mco.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/mc/7mco ftp://data.pdbj.org/pub/pdb/validation_reports/mc/7mco	HTTPS FTP

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Related structure data

Related structure data	7lvyC 6pntS S: Starting model for refinement C: citing same article (ref.)
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 203A2

B: UDP-glycosyltransferase 203A2

hetero molecules

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

1

A: UDP-glycosyltransferase 203A2

hetero molecules

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

2

B: UDP-glycosyltransferase 203A2

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.189, 66.085, 75.971
Angle α, β, γ (deg.)	88.544, 72.780, 87.401
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 0 - 426 / Label seq-ID: 35 - 461

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

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

#1: Protein	UDP-glycosyltransferase 203A2 Mass: 52697.293 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite) Gene: 107359436, UGT203A2 / Production host: Escherichia coli (E. coli) / References: UniProt: T1K1R5
#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine 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: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 826 / 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: 2.19 Å³/Da / Density % sol: 43.84 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Sodium Chloride, 0.1 M Bis-tris pH 5.5, 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: May 29, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 55037 / % possible obs: 90.6 % / Redundancy: 2.1 % / CC_1/2: 0.998 / CC star: 0.999 / R_merge(I) obs: 0.049 / R_pim(I) all: 0.044 / R_rim(I) all: 0.066 / R_sym value: 0.049 / Net I/σ(I): 16.45
Reflection shell	Resolution: 2→2.03 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.232 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 2775 / CC_1/2: 0.883 / CC star: 0.965 / R_pim(I) all: 0.22 / R_rim(I) all: 0.33 / R_sym value: 0.232 / % possible all: 91.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
HKL-3000		data reduction
HKL-3000		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6PNT

6pnt

Resolution: 2→29.92 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.94 / SU B: 7.399 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.202 / ESU R Free: 0.165
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2033	2720	4.968 %
R_work	0.1575	52029	-
all	0.16	-	-
obs	-	54749	90.602 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 25.639 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.05 Å²	-0.126 Å²	-0.078 Å²
2-	-	-0.063 Å²	-0.349 Å²
3-	-	-	-0.038 Å²

Refinement step

Cycle: LAST / Resolution: 2→29.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6851	0	50	826	7727

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	7126
X-RAY DIFFRACTION	r_bond_other_d	0.034	0.017	6768
X-RAY DIFFRACTION	r_angle_refined_deg	1.533	1.65	9657
X-RAY DIFFRACTION	r_angle_other_deg	2.238	1.588	15694
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.988	5	862
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.317	23.149	362
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.038	15	1263
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.612	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	916
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	7924
X-RAY DIFFRACTION	r_gen_planes_other	0.012	0.02	1560
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1450
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	6145
X-RAY DIFFRACTION	r_nbtor_refined	0.167	0.2	3530
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.065	0.2	2955
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	646
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.07	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.166	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.266	0.2	79
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.189	0.2	36
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.066	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.163	1.697	3439
X-RAY DIFFRACTION	r_mcbond_other	1.161	1.696	3438
X-RAY DIFFRACTION	r_mcangle_it	1.809	2.537	4304
X-RAY DIFFRACTION	r_mcangle_other	1.809	2.538	4305
X-RAY DIFFRACTION	r_scbond_it	1.542	1.922	3687
X-RAY DIFFRACTION	r_scbond_other	1.542	1.922	3686
X-RAY DIFFRACTION	r_scangle_it	2.487	2.799	5353
X-RAY DIFFRACTION	r_scangle_other	2.486	2.799	5354
X-RAY DIFFRACTION	r_lrange_it	5.072	21.73	8245
X-RAY DIFFRACTION	r_lrange_other	4.916	20.955	8034
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.09	0.05	13860

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	0.08992	0.05007
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08992	0.05007

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.052	0.244	226	0.198	3868	X-RAY DIFFRACTION	92.332
2.052-2.108	0.245	218	0.18	3862	X-RAY DIFFRACTION	93.578
2.108-2.169	0.218	204	0.176	3755	X-RAY DIFFRACTION	93.3726
2.169-2.235	0.263	195	0.188	3455	X-RAY DIFFRACTION	89.813
2.235-2.308	0.251	128	0.203	3292	X-RAY DIFFRACTION	84.8004
2.308-2.389	0.195	145	0.152	3316	X-RAY DIFFRACTION	90.6496
2.389-2.479	0.211	181	0.156	3023	X-RAY DIFFRACTION	85.7602
2.479-2.58	0.245	168	0.164	3057	X-RAY DIFFRACTION	90.7173
2.58-2.694	0.201	154	0.151	3127	X-RAY DIFFRACTION	95.0188
2.694-2.825	0.186	146	0.147	2961	X-RAY DIFFRACTION	94.9862
2.825-2.977	0.211	153	0.157	2807	X-RAY DIFFRACTION	94.5385
2.977-3.156	0.186	110	0.149	2613	X-RAY DIFFRACTION	92.7452
3.156-3.373	0.194	100	0.162	2415	X-RAY DIFFRACTION	90.4676
3.373-3.641	0.204	101	0.156	1948	X-RAY DIFFRACTION	78.9291
3.641-3.985	0.184	137	0.144	1854	X-RAY DIFFRACTION	83.6906
3.985-4.45	0.173	83	0.128	1928	X-RAY DIFFRACTION	93.5784
4.45-5.128	0.204	98	0.139	1638	X-RAY DIFFRACTION	91.8033
5.128-6.255	0.176	77	0.162	1383	X-RAY DIFFRACTION	90.9657
6.255-8.739	0.164	67	0.145	1062	X-RAY DIFFRACTION	90.5373
8.739-29.9	0.149	27	0.143	650	X-RAY DIFFRACTION	93.2507

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	0.4705	0.6388	-0.2484	1.6713	-0.4277	1.0101	0.0024	0.0556	0.0955	0.0361	0.1165	0.1554	-0.1577	-0.2018	-0.1189	0.0648	0.0637	0.0157	0.0695	0.0276	0.0253	-8.173	24.178	-21.944
2	0.399	0.0484	0.1502	1.0254	0.0327	0.8763	0.0139	0.076	0.0389	-0.0666	0.0366	-0.0264	-0.0357	0.0173	-0.0505	0.0757	0.0405	0.0197	0.0477	0.0125	0.0129	1.005	18.854	-30.848
3	2.6427	-2.9849	1.0424	7.837	-2.9212	2.1504	0.066	0.1596	-0.0587	-0.4101	0.0455	0.0875	0.1133	0.0806	-0.1115	0.106	0.0359	-0.0002	0.0683	-0.0108	0.0075	1.276	11.832	-40.984
4	0.4565	0.0802	-0.2214	0.6947	-0.1483	1.1144	0.022	-0.0262	-0.016	0.1457	0.0727	-0.0464	0.0462	0.0162	-0.0947	0.0799	0.0566	-0.0182	0.0487	-0.0054	0.0155	-0.188	11.403	-8.999
5	2.1143	-0.0695	1.1783	6.1203	-7.2224	16.8306	-0.081	0.0435	0.2076	-0.0119	-0.1034	-0.202	-0.0216	0.4037	0.1844	0.0349	-0.0228	0.0007	0.0298	-0.0017	0.0353	13.785	35.574	-24.656
6	1.9469	-1.2203	0.6486	2.2451	-0.1857	1.2694	-0.0418	0.0623	0.0524	-0.1028	0.0579	-0.134	-0.1205	0.2574	-0.0161	0.0738	0.0099	0.018	0.09	-0.0014	0.0104	9.141	-5.365	21.819
7	1.3514	-0.0223	-0.0604	4.1517	2.544	1.5757	-0.089	-0.0705	-0.1969	0.3585	0.0285	0.0866	0.2778	0.0573	0.0605	0.2441	0.133	0.0169	0.1005	0.0218	0.0386	5.918	-29.417	28.304
8	0.6301	0.1438	0.3158	1.0699	0.3877	1.0111	-0.0533	-0.1026	-0.0561	0.0925	0.0196	0.063	0.0606	-0.0088	0.0336	0.0722	0.0595	0.0286	0.0566	0.0249	0.0159	-5.523	-14.581	30.133
9	1.2171	-0.0424	-0.2226	0.9968	0.4348	1.3594	-0.0626	0.041	-0.0787	-0.1037	0.1219	-0.0516	0.021	0.1812	-0.0593	0.1103	0.0438	0.0098	0.0736	-0.0255	0.0222	5.859	-23.9	5.988
10	1.2641	-0.9424	0.2788	3.6843	1.6177	2.0339	-0.1079	0.0775	-0.116	-0.2679	-0.0725	0.3774	-0.1217	-0.0505	0.1804	0.0806	-0.0007	-0.006	0.0374	0.0098	0.0576	-7.878	-17.045	8.989

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 86
2	X-RAY DIFFRACTION	2	ALL	A	87 - 172
3	X-RAY DIFFRACTION	3	ALL	A	173 - 203
4	X-RAY DIFFRACTION	4	ALL	A	204 - 410
5	X-RAY DIFFRACTION	5	ALL	A	411 - 426
6	X-RAY DIFFRACTION	6	ALL	B	1 - 70
7	X-RAY DIFFRACTION	7	ALL	B	71 - 100
8	X-RAY DIFFRACTION	8	ALL	B	101 - 243
9	X-RAY DIFFRACTION	9	ALL	B	244 - 371
10	X-RAY DIFFRACTION	10	ALL	B	372 - 425

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