PDB-7es2: a mutant of glycosyktransferase in complex with UDP and Reb D

ID or keywords:

Entry

Database: PDB / ID: 7es2

Title

a mutant of glycosyktransferase in complex with UDP and Reb D

Components

Glycosyltransferase

Keywords

TRANSFERASE / H27A mutant / 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: 2.34 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	7es2.cif.gz	166.7 KB	Display	PDBx/mmCIF format
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PDBx/mmJSON format	7es2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/es/7es2 ftp://data.pdbj.org/pub/pdb/validation_reports/es/7es2	HTTPS FTP

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Related structure data

Related structure data	7erxC 7eryC 7es0C 7es1C C: citing same article (ref.)
Similar structure data	7erx-d 2vn8-1 5qd6-3 4lxa-3 7es1-d 1qmu-d 3zm4-d 4l7g-d 1eoa-d 2buq-d 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

52.5 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)	54.444, 83.496, 110.645
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: 50975.430 Da / Num. of mol.: 1 / Mutation: H27A 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-JDO / rebaudioside D Mass: 1129.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅₀H₈₀O₂₈ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.52 Å³/Da / Density % sol: 51.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 4000 and 0.1 M HEPES pH6.5

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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: Jun 26, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 2.34→36.88 Å / Num. obs: 21963 / % possible obs: 100 % / Redundancy: 6 % / CC_1/2: 0.977 / R_merge(I) obs: 0.06 / Net I/σ(I): 15.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	Diffraction-ID	% possible all
6.34-36.89	5.2	0.027	1220	0.945	1	100
2.34-2.38		0.22	1102	0.983	1

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: apo form of this protein

Resolution: 2.34→35.215 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.942 / SU B: 23.933 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.228
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.243	1076	4.909 %
R_work	0.1963	20843	-
all	0.199	-	-
obs	-	21919	99.786 %

Solvent computation

Ion probe radii: 1.11 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 58.905 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.819 Å²	0 Å²	0 Å²
2-	-	-2.024 Å²	0 Å²
3-	-	-	-3.795 Å²

Refinement step

Cycle: LAST / Resolution: 2.34→35.215 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3088	0	103	30	3221

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	3285
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	3133
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	1.65	4490
X-RAY DIFFRACTION	r_angle_other_deg	1.12	1.573	7220
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.503	5	405
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.113	20.062	162
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	1.739	10	1
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.995	15	507
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.566	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.048	0.2	439
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	3601
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	731
X-RAY DIFFRACTION	r_nbd_refined	0.189	0.2	639
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.172	0.2	2937
X-RAY DIFFRACTION	r_nbtor_refined	0.15	0.2	1560
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1496
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.106	0.2	85
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.164	0.2	2
X-RAY DIFFRACTION	r_nbd_other	0.151	0.2	26
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.12	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	3.629	3.69	1623
X-RAY DIFFRACTION	r_mcbond_other	3.623	3.688	1622
X-RAY DIFFRACTION	r_mcangle_it	5.034	5.542	2027
X-RAY DIFFRACTION	r_mcangle_other	5.032	5.544	2028
X-RAY DIFFRACTION	r_scbond_it	4.639	4.397	1662
X-RAY DIFFRACTION	r_scbond_other	4.638	4.4	1663
X-RAY DIFFRACTION	r_scangle_it	6.653	6.463	2463
X-RAY DIFFRACTION	r_scangle_other	6.651	6.466	2464
X-RAY DIFFRACTION	r_lrange_it	7.857	45.954	3451
X-RAY DIFFRACTION	r_lrange_other	7.861	45.943	3449

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 (%)
2.34-2.401	0.362	84	0.316	1513	X-RAY DIFFRACTION	99.7502
2.401-2.466	0.383	84	0.303	1469	X-RAY DIFFRACTION	100
2.466-2.537	0.37	77	0.309	1415	X-RAY DIFFRACTION	100
2.537-2.615	0.298	54	0.269	1433	X-RAY DIFFRACTION	100
2.615-2.7	0.308	70	0.263	1349	X-RAY DIFFRACTION	100
2.7-2.794	0.335	74	0.237	1294	X-RAY DIFFRACTION	99.927
2.794-2.899	0.238	67	0.223	1261	X-RAY DIFFRACTION	99.9248
2.899-3.017	0.349	76	0.231	1221	X-RAY DIFFRACTION	99.923
3.017-3.15	0.268	70	0.234	1161	X-RAY DIFFRACTION	99.9188
3.15-3.303	0.238	56	0.207	1117	X-RAY DIFFRACTION	99.8298
3.303-3.48	0.263	59	0.215	1065	X-RAY DIFFRACTION	99.7338
3.48-3.689	0.281	51	0.195	1028	X-RAY DIFFRACTION	99.7227
3.689-3.941	0.229	37	0.179	972	X-RAY DIFFRACTION	99.6051
3.941-4.252	0.191	46	0.155	892	X-RAY DIFFRACTION	99.5754
4.252-4.652	0.158	43	0.128	836	X-RAY DIFFRACTION	99.2099
4.652-5.191	0.15	38	0.143	763	X-RAY DIFFRACTION	99.5031
5.191-5.974	0.232	24	0.162	692	X-RAY DIFFRACTION	99.7215
5.974-7.269	0.225	32	0.167	576	X-RAY DIFFRACTION	100
7.269-10.086	0.187	18	0.143	481	X-RAY DIFFRACTION	99.8
10.086-35.21	0.177	16	0.205	305	X-RAY DIFFRACTION	100

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	0.3714	-0.0425	0.3846	2.826	-0.8568	3.1664	0.078	-0.0054	0.0931	-0.1178	0.0328	0.3684	-0.1636	-0.3966	-0.1109	0.4285	0.0152	0.0062	0.0607	0.0244	0.1084	-13.857	18.129	-31.022
2	0.4887	-1.3113	0.1019	4.1677	-0.8204	5.2987	0.1151	0.0396	-0.092	-0.2178	0.0152	-0.0663	0.2397	0.1348	-0.1304	0.3884	0.0102	-0.0481	0.0379	-0.0855	0.2019	-3.811	2.069	-34.142
3	5.1124	-0.3507	-4.4668	6.6971	5.3225	7.6966	0.1018	0.1306	0.131	0.056	0.1155	-0.039	0.0036	-0.0341	-0.2173	0.5792	-0.0229	-0.0325	0.0242	0.0552	0.2882	-1.799	21.183	-12.971
4	0.9089	-0.2801	-0.5519	1.9436	-0.2649	3.6578	-0.0711	-0.0073	-0.0539	0.2401	0.1779	0.1302	0.0718	-0.1048	-0.1067	0.4155	0.0034	0.0161	0.0193	0.0108	0.0273	-9.104	4.53	-6.947
5	3.6603	0.4734	-1.6681	3.2015	-1.8667	4.7642	-0.1781	-0.1277	-0.0206	0.233	0.0652	-0.2927	0.317	0.6927	0.1128	0.5517	0.0744	-0.026	0.1539	-0.0202	0.038	0.046	-3.588	-8.853
6	3.6419	0.8339	1.5737	3.4877	-2.0763	8.8771	0.1495	0.2088	0.1427	-0.0974	-0.1009	-0.22	-0.0637	0.3254	-0.0486	0.2403	0.0152	0.065	0.1723	0.0327	0.1932	6.835	14.268	-34.84

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	15 - 150
2	X-RAY DIFFRACTION	2	ALL	A	151 - 249
3	X-RAY DIFFRACTION	3	ALL	A	250 - 260
4	X-RAY DIFFRACTION	4	ALL	A	261 - 400
5	X-RAY DIFFRACTION	5	ALL	A	401 - 445
6	X-RAY DIFFRACTION	6	ALL	A	446 - 459

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