PDB-7es1: glycosyltransferase in complex with UDP and ST

ID or keywords:

Entry

Database: PDB / ID: 7es1

Title

glycosyltransferase in complex with UDP and ST

Components

Glycosyltransferase

Keywords

TRANSFERASE / a rice glycosyltransferase

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: 1.66 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	Apr 3, 2024	Group: Data collection / Derived calculations / Refinement description Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7es1.cif.gz	171.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7es1.ent.gz	128.6 KB	Display	PDB format
PDBx/mmJSON format	7es1.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	7es1_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	7es1_full_validation.pdf.gz	1.1 MB	Display
Data in XML	7es1_validation.xml.gz	20.1 KB	Display
Data in CIF	7es1_validation.cif.gz	31 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/7es1 ftp://data.pdbj.org/pub/pdb/validation_reports/es/7es1	HTTPS FTP

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Related structure data

Related structure data	7erxC 7eryC 7es0C 7es2C 7er0 C: citing same article (ref.)
Similar structure data	7es0-d 7es2-d 2hm1-d 2vh4-2 3vfc-d 5wxv-4 3iaa-3 2zcj-d 4lxa-3 3djd-2 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

51.9 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)	50.843, 83.042, 109.167
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#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
#2: 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
#3: Chemical	ChemComp-JDF / steviol-19-o-glucoside Mass: 480.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₆H₄₀O₈ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.31 Å³/Da / Density % sol: 46.66 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000 and 0.1 M HEPES 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: 1.66→46.09 Å / Num. obs: 55463 / % possible obs: 99.9 % / Redundancy: 5.9 % / CC_1/2: 0.996 / R_merge(I) obs: 0.089 / Net I/σ(I): 9

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	% possible all
4.5-46.11	5.8	0.07	20.9	3020	0.992	100
1.66-1.69	3.2	1.087		2623	0.499	96.8

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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
Starting model: apo form of this protein

Resolution: 1.66→46.089 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.96 / SU B: 4.428 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2043	2734	4.937 %
R_work	0.1788	52643	-
all	0.18	-	-
obs	-	55377	99.775 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 29.627 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.38 Å²	0 Å²	0 Å²
2-	-	-0.4 Å²	-0 Å²
3-	-	-	-0.98 Å²

Refinement step

Cycle: LAST / Resolution: 1.66→46.089 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3122	0	59	397	3578

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	3294
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3138
X-RAY DIFFRACTION	r_angle_refined_deg	1.438	1.646	4501
X-RAY DIFFRACTION	r_angle_other_deg	1.351	1.575	7224
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.444	5	414
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.525	20.364	165
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.444	10	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.735	15	516
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.521	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	425
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	3688
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	742
X-RAY DIFFRACTION	r_nbd_refined	0.202	0.2	663
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	2894
X-RAY DIFFRACTION	r_nbtor_refined	0.159	0.2	1601
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	1482
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.116	0.2	315
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.011	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.17	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.191	0.2	27
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.176	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.902	1.476	1650
X-RAY DIFFRACTION	r_mcbond_other	0.902	1.473	1649
X-RAY DIFFRACTION	r_mcangle_it	1.626	2.205	2066
X-RAY DIFFRACTION	r_mcangle_other	1.625	2.209	2067
X-RAY DIFFRACTION	r_scbond_it	0.999	1.689	1644
X-RAY DIFFRACTION	r_scbond_other	0.999	1.69	1645
X-RAY DIFFRACTION	r_scangle_it	1.694	2.483	2435
X-RAY DIFFRACTION	r_scangle_other	1.693	2.484	2436
X-RAY DIFFRACTION	r_lrange_it	6.311	20.211	3773
X-RAY DIFFRACTION	r_lrange_other	6.19	18.71	3638

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
1.659-1.702	0.319	176	0.314	3786	0.314	4055	0.594	0.617	97.7065	0.307
1.702-1.749	0.283	193	0.277	3714	0.278	3915	0.774	0.781	99.7957	0.263
1.749-1.799	0.303	191	0.247	3668	0.249	3859	0.83	0.858	100	0.228
1.799-1.855	0.259	204	0.22	3507	0.222	3713	0.897	0.905	99.9461	0.199
1.855-1.915	0.248	184	0.215	3445	0.216	3631	0.897	0.916	99.9449	0.191
1.915-1.982	0.23	159	0.196	3331	0.197	3493	0.923	0.933	99.9141	0.174
1.982-2.057	0.219	143	0.188	3239	0.189	3386	0.933	0.941	99.8819	0.17
2.057-2.141	0.208	184	0.18	3096	0.182	3280	0.943	0.951	100	0.164
2.141-2.236	0.19	137	0.176	2976	0.176	3114	0.954	0.956	99.9679	0.162
2.236-2.345	0.17	146	0.157	2864	0.158	3010	0.961	0.964	100	0.147
2.345-2.471	0.201	142	0.162	2727	0.164	2869	0.953	0.96	100	0.157
2.471-2.621	0.198	137	0.159	2577	0.161	2714	0.95	0.962	100	0.156
2.621-2.801	0.232	114	0.159	2464	0.162	2578	0.946	0.962	100	0.162
2.801-3.024	0.19	120	0.16	2249	0.161	2369	0.955	0.965	100	0.167
3.024-3.312	0.19	111	0.172	2101	0.173	2212	0.957	0.96	100	0.185
3.312-3.7	0.228	119	0.173	1892	0.176	2011	0.942	0.962	100	0.19
3.7-4.268	0.17	98	0.157	1706	0.158	1804	0.967	0.971	100	0.181
4.268-5.216	0.144	75	0.162	1458	0.161	1535	0.979	0.975	99.8697	0.198
5.216-7.33	0.206	61	0.204	1158	0.204	1219	0.957	0.961	100	0.238
7.33-46.089	0.239	40	0.186	684	0.189	732	0.948	0.957	98.9071	0.33

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	0.8301	-0.9655	-0.1488	1.5076	0.1261	0.8175	-0.0396	0.043	0.0183	0.1771	0.0365	-0.0819	-0.3609	0.1662	0.0031	0.2941	-0.0289	-0.0364	0.1497	-0.0154	0.1255	14.132	15.857	30.269
2	2.5119	-1.0275	-0.0124	0.826	0.2882	2.7291	-0.163	0.0457	-0.0513	0.3091	0.0911	-0.0869	-0.3192	0.291	0.0719	0.2889	-0.0087	-0.0793	0.0687	-0.0279	0.0619	14.582	15.224	42.264
3	0.247	0.1833	0.5846	0.256	0.6619	3.1186	0.0079	-0.0055	-0.0646	0.0944	0.0276	0.0191	-0.165	-0.095	-0.0355	0.2219	0.0351	-0.0107	0.1355	-0.0071	0.1442	2.767	3.589	36.441
4	2.279	-0.0369	0.3502	3.6885	1.9282	5.1822	0.2421	0.1334	0.343	-0.3898	-0.0773	-0.0126	-0.8687	-0.1683	-0.1648	0.3454	0.0178	0.0786	0.0203	0.0271	0.0629	11.102	14.059	5.238
5	0.3996	-0.1722	-0.099	0.519	0.5732	1.7162	0.024	-0.0709	0.0365	-0.0985	0.0762	-0.048	-0.0666	0.1755	-0.1002	0.1645	-0.0144	0.0047	0.1556	-0.0153	0.1129	15.035	-0.663	11.759
6	0.7632	-0.244	-0.5553	1.2256	0.8594	2.3753	-0.038	0.1421	0.0231	-0.0765	-0.0683	0.1415	-0.0679	-0.2173	0.1063	0.116	0.0212	-0.0398	0.08	0.0093	0.0854	0.118	0.326	17.058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	15 - 100
2	X-RAY DIFFRACTION	2	ALL	A	101 - 124
3	X-RAY DIFFRACTION	3	ALL	A	125 - 251
4	X-RAY DIFFRACTION	4	ALL	A	252 - 273
5	X-RAY DIFFRACTION	5	ALL	A	274 - 401
6	X-RAY DIFFRACTION	6	ALL	A	402 - 462

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