PDB-7es0: a rice glycosyltransferase in complex with UDP and REX

ID or keywords:

Entry

Database: PDB / ID: 7es0

Title

a rice glycosyltransferase in complex with UDP and REX

Components

Glycosyltransferase

Keywords

TRANSFERASE / steviol glucosylation

Function / homology

Function and homology information

UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding
Similarity search - Function

Biological species

Oryza sativa subsp. japonica (Japanese rice)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.395 Å

Authors

Zhu, X.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2021
Title: Catalytic flexibility of rice glycosyltransferase OsUGT91C1 for the production of palatable steviol glycosides.
Authors: Zhang, J. / Tang, M. / Chen, Y. / Ke, D. / Zhou, J. / Xu, X. / Yang, W. / He, J. / Dong, H. / Wei, Y. / Naismith, J.H. / Lin, Y. / Zhu, X. / Cheng, W.

History

Deposition	May 8, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 15, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	May 29, 2024	Group: Data collection / Derived calculations / Category: atom_type / chem_comp_atom / chem_comp_bond / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7es0.cif.gz	170.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7es0_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7es0_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7es0_validation.xml.gz	21.3 KB	Display
Data in CIF	7es0_validation.cif.gz	33.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/7es0 ftp://data.pdbj.org/pub/pdb/validation_reports/es/7es0	HTTPS FTP

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Related structure data

Related structure data	7erxC 7eryC 7es1C 7es2C C: citing same article (ref.)
Similar structure data	7es1-d 3djd-2 3vfc-d 6l5n-2 7es2-d 7ery-d 1eoc-d 5wxv-4 2bum-d 3djd-1 Search similar-shape structures by Omokage search (details) 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: Glycosyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	57.561, 83.082, 87.946
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 1 molecules A

#1: Protein	Glycosyltransferase Mass: 51042.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Os03g0702000, OSNPB_030702000 / Production host: Escherichia coli (E. coli) References: UniProt: Q0DPB7, Transferases; Glycosyltransferases; Hexosyltransferases

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Non-polymers , 6 types, 488 molecules

#2: Chemical	ChemComp-3E6 / Rebaudioside A2 Mass: 967.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₄H₇₀O₂₃
#3: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#4: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID Mass: 209.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.1 Å³/Da / Density % sol: 41.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000 0.1 M HEPES buffer pH 6.5

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.978 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 1.39→57.56 Å / Num. obs: 58677 / % possible obs: 69.4 % / Redundancy: 5.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.04 / Net I/σ(I): 22.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	Diffraction-ID	% possible all
3.79-57.61	6	0.017	4537	1	1	100
1.39-1.42	1.3	0.303	185	0.82	1	4.4

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS		data reduction
PHASER		phasing
DIALS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.395→48.209 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.965 / SU B: 2.028 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.073
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1745	3065	5.228 %
R_work	0.1586	55563	-
all	0.16	-	-
obs	-	58628	69.333 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 17.086 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.03 Å²	-0 Å²	0 Å²
2-	-	-0.777 Å²	-0 Å²
3-	-	-	-0.253 Å²

Refinement step

Cycle: LAST / Resolution: 1.395→48.209 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3115	0	119	482	3716

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	3371
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3224
X-RAY DIFFRACTION	r_angle_refined_deg	1.358	1.651	4604
X-RAY DIFFRACTION	r_angle_other_deg	1.346	1.573	7431
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.545	5	417
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.436	19.941	169
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.136	10	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.825	15	524
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.364	15	32
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	442
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3709
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	755
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	699
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.17	0.2	3015
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	1639
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1534
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.101	0.2	367
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.125	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.183	0.2	73
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.11	0.2	31
X-RAY DIFFRACTION	r_mcbond_it	1.113	1.335	1656
X-RAY DIFFRACTION	r_mcbond_other	1.099	1.333	1655
X-RAY DIFFRACTION	r_mcangle_it	1.81	2	2077
X-RAY DIFFRACTION	r_mcangle_other	1.81	2.002	2078
X-RAY DIFFRACTION	r_scbond_it	1.631	1.57	1715
X-RAY DIFFRACTION	r_scbond_other	1.631	1.57	1716
X-RAY DIFFRACTION	r_scangle_it	2.563	2.263	2527
X-RAY DIFFRACTION	r_scangle_other	2.562	2.263	2528
X-RAY DIFFRACTION	r_lrange_it	4.604	18.009	3894
X-RAY DIFFRACTION	r_lrange_other	4.336	16.741	3725

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 (%)
1.395-1.431	0.267	23	0.261	409	X-RAY DIFFRACTION	7.005
1.431-1.47	0.256	67	0.226	1027	X-RAY DIFFRACTION	18.1366
1.47-1.513	0.236	75	0.211	1540	X-RAY DIFFRACTION	27.466
1.513-1.559	0.205	128	0.189	2021	X-RAY DIFFRACTION	37.7747
1.559-1.611	0.209	113	0.175	2445	X-RAY DIFFRACTION	46.4078
1.611-1.667	0.208	173	0.169	2869	X-RAY DIFFRACTION	56.8811
1.667-1.73	0.193	193	0.166	3491	X-RAY DIFFRACTION	71.4092
1.73-1.8	0.176	224	0.158	4357	X-RAY DIFFRACTION	91.4554
1.8-1.88	0.209	246	0.165	4457	X-RAY DIFFRACTION	98.6367
1.88-1.972	0.186	219	0.163	4314	X-RAY DIFFRACTION	98.8228
1.972-2.079	0.184	181	0.154	4128	X-RAY DIFFRACTION	98.853
2.079-2.205	0.186	203	0.153	3919	X-RAY DIFFRACTION	99.2775
2.205-2.357	0.174	213	0.152	3635	X-RAY DIFFRACTION	99.3802
2.357-2.545	0.158	239	0.145	3381	X-RAY DIFFRACTION	99.3141
2.545-2.787	0.182	177	0.144	3163	X-RAY DIFFRACTION	99.1098
2.787-3.115	0.174	159	0.151	2873	X-RAY DIFFRACTION	99.8354
3.115-3.596	0.172	124	0.164	2604	X-RAY DIFFRACTION	99.9267
3.596-4.399	0.148	124	0.153	2212	X-RAY DIFFRACTION	99.8717
4.399-6.204	0.155	108	0.166	1704	X-RAY DIFFRACTION	99.9448
6.204-48.2	0.171	76	0.182	1015	X-RAY DIFFRACTION	99.9084

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	0.2241	-0.1876	0.0438	0.1724	-0.0256	0.1902	-0.0077	0.0158	-0.0142	0.0257	-0.008	0.0038	0.0385	-0.0158	0.0157	0.0297	0.0004	-0.0096	0.0077	-0.0007	0.0257	-12.8091	-26.5713	21.7561
2	0.381	-0.343	-0.0045	0.3269	0.0434	0.1884	-0.0384	-0.0471	0.0081	0.0554	0.0178	-0.0046	0.0085	-0.067	0.0206	0.0431	-0.0162	-0.0007	0.0447	-0.0016	0.0095	-16.997	-20.8157	32.2803
3	0.085	-0.054	-0.0276	0.0532	0.0305	0.3371	0.0206	-0.0115	0.0165	0.0106	0.0012	-0.0155	0.0252	0.0045	-0.0218	0.0362	-0.0092	-0.0043	0.0057	-0.0052	0.0278	-3.1927	-11.8523	25.7212
4	0.2344	-0.075	0.1213	0.0309	-0.0611	0.3264	0.0347	0.0218	0.0127	-0.0077	-0.0115	0.0022	0.0085	0.0155	-0.0232	0.0213	0.0066	0.0005	0.0082	-0.002	0.0164	-9.3121	-10.1474	2.172
5	0.8374	-0.1459	0.2369	0.2557	-0.2316	0.2721	-0.0783	0.0721	0.1083	0.0248	-0.003	-0.0502	-0.0831	0.0414	0.0813	0.0733	-0.0305	-0.0226	0.0245	0.0281	0.0472	-2.3178	1.0448	0.0638
6	1.1298	0.0113	0.0685	0.6763	-1.46	3.2413	0.017	0.0097	-0.119	-0.0435	-0.0552	-0.0596	0.1089	0.127	0.0383	0.0166	0.014	-0.0104	0.0125	-0.0039	0.0961	8.4478	-18.5652	20.3133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	15 - 94
2	X-RAY DIFFRACTION	2	ALL	A	95 - 147
3	X-RAY DIFFRACTION	3	ALL	A	148 - 260
4	X-RAY DIFFRACTION	4	ALL	A	261 - 400
5	X-RAY DIFFRACTION	5	ALL	A	401 - 432
6	X-RAY DIFFRACTION	6	ALL	A	433 - 458

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