PDB-9kpw: UDP-glycosyltransferase TsUGT1 with UDP

ID or keywords:

Entry

Database: PDB / ID: 9kpw

Title

UDP-glycosyltransferase TsUGT1 with UDP

Components

Glycosyltransferase

Keywords

TRANSFERASE / UDP-glycosyltransferase / glucoside ester bond / deglycosylation

Function / homology

UDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / membrane / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase

Function and homology information

Biological species

Trifolium subterraneum (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Feng, X. / Sun, Q.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Investigation of the bond cleavage mechanism of UDP-glycosyltransferase
Authors: Feng, X. / Sun, Q.

History

Deposition	Nov 24, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 26, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kpw.cif.gz	890.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9kpw.ent.gz	614.5 KB	Display	PDB format
PDBx/mmJSON format	9kpw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9kpw_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	9kpw_full_validation.pdf.gz	1.6 MB	Display
Data in XML	9kpw_validation.xml.gz	73.9 KB	Display
Data in CIF	9kpw_validation.cif.gz	94.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kp/9kpw ftp://data.pdbj.org/pub/pdb/validation_reports/kp/9kpw	HTTPS FTP

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Related structure data

Related structure data	9kpxC 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: Glycosyltransferase

B: Glycosyltransferase

C: Glycosyltransferase

D: Glycosyltransferase

hetero molecules

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

1

A: Glycosyltransferase

hetero molecules

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

2

B: Glycosyltransferase

hetero molecules

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

3

C: Glycosyltransferase

hetero molecules

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

4

D: Glycosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.746, 89.258, 113.182
Angle α, β, γ (deg.)	93.744, 97.612, 104.312
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Glycosyltransferase / UDP-glycosyltransferase TsUGT1 Mass: 53091.742 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trifolium subterraneum (plant) / Gene: TSUD_196840 / Production host: Escherichia coli (E. coli) References: UniProt: A0A2Z6NA72, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 46.67 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion / pH: 7.5 / Details: 20mM Tris 100mM NaCl, 5mM DTT

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 29, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.75→28.68 Å / Num. obs: 88146 / % possible obs: 91.17 % / Redundancy: 2 % / B_iso Wilson estimate: 34.71 Å² / CC_1/2: 0.984 / CC star: 0.996 / R_merge(I) obs: 0.076 / Net I/σ(I): 6.82
Reflection shell	Resolution: 2.75→2.848 Å / Num. unique obs: 9584 / CC_1/2: 0.861 / CC star: 0.962 / % possible all: 97.34

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Processing

Software

Name	Version	Classification
PHENIX	1.15.1_3469	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.75→28.68 Å / SU ML: 0.3545 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 26.1001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2472	2260	5.02 %
R_work	0.1903	42730	-
obs	0.1932	44990	91.25 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 37.65 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→28.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14960	0	100	218	15278

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	15444
X-RAY DIFFRACTION	f_angle_d	0.4714	20968
X-RAY DIFFRACTION	f_chiral_restr	0.0402	2296
X-RAY DIFFRACTION	f_plane_restr	0.0037	2692
X-RAY DIFFRACTION	f_dihedral_angle_d	14.9987	9171

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 (%)
2.75-2.81	0.3131	163	0.2411	2859	X-RAY DIFFRACTION	96.98
2.81-2.88	0.3019	148	0.2357	2836	X-RAY DIFFRACTION	97.84
2.88-2.95	0.356	146	0.2385	2859	X-RAY DIFFRACTION	97.22
2.95-3.03	0.3117	127	0.2388	2875	X-RAY DIFFRACTION	97.88
3.03-3.12	0.3006	153	0.2368	2850	X-RAY DIFFRACTION	97.56
3.12-3.22	0.3164	150	0.2307	2869	X-RAY DIFFRACTION	97.99
3.22-3.33	0.2972	163	0.2216	2872	X-RAY DIFFRACTION	97.84
3.33-3.46	0.3083	90	0.2229	1601	X-RAY DIFFRACTION	95.97
3.46-3.62	0.2733	148	0.1999	2831	X-RAY DIFFRACTION	96.78
3.62-3.81	0.2662	83	0.1797	1855	X-RAY DIFFRACTION	63.62
3.81-4.05	0.2	102	0.1661	2053	X-RAY DIFFRACTION	69.61
4.05-4.36	0.1971	164	0.1585	2888	X-RAY DIFFRACTION	98.42
4.36-4.8	0.2018	152	0.1459	2859	X-RAY DIFFRACTION	98.56
4.8-5.49	0.2324	163	0.1654	2848	X-RAY DIFFRACTION	98.4
5.49-6.9	0.1974	150	0.1804	2927	X-RAY DIFFRACTION	99.1
6.9-28.68	0.1824	158	0.1635	2848	X-RAY DIFFRACTION	97.5

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	2.45435593192	0.465462302584	1.13622993551	1.33631391019	-0.195085394147	2.6022712232	0.0290034829975	0.239469482044	0.053316146511	-0.0819152965296	0.000720101908806	-0.0971447089973	-0.088893848499	0.0882115919411	-0.0325709759385	0.190204461177	0.0294696150126	0.0623889095506	0.23148805381	0.018381280372	0.192098118625	12.8154827744	-39.7013672473	-1.14389994797
2	1.15334466327	-0.303575801776	0.0586318095599	0.173588796308	0.108590904482	0.421995060867	0.0481419027203	0.140574013294	-0.0313498253209	0.0163044461376	-0.016576015847	0.0123596616154	0.0266860555914	-0.0830413112446	-0.0359500425711	0.216605141746	-0.0178228945492	0.03297994932	0.232732413674	0.0078317790757	0.248929347727	5.12098096286	-45.6300453662	16.1172879902
3	0.70095140199	0.935314851859	0.253055715143	2.21463271538	0.282582894263	1.00509064836	0.0209057234115	-0.103909151014	-0.0154177313613	0.165823529456	-0.0480304285577	-0.298573110206	-0.0967359571124	0.21778395484	0.0127883901754	0.163219882924	0.0265548190884	-0.0204636910097	0.296158355357	-0.0291005765462	0.228917728945	25.9880892995	-41.6745647828	29.7219419036
4	1.43558002648	0.0442074609783	0.821644116515	0.772957234907	0.424055640001	1.99698125158	0.0826521802057	-0.0184995552316	-0.0841868552064	0.0386489341031	0.043554624676	0.0190428284307	0.214004579247	-0.108639260401	-0.142967549709	0.171911909211	-0.0377362957162	0.0298279773067	0.142154824536	0.000590922773504	0.178142328057	6.74520781003	-49.9158413646	19.80874288
5	2.39086000023	-0.533232911245	0.347224372128	1.38970243038	-0.194377370498	2.26804383216	-0.0162964394302	-0.261226709531	0.00984411416409	0.122351355898	0.0179813319065	0.0548092263517	-0.0141764590119	-0.13346680603	-0.00406720539816	0.176395657175	-0.0379867494797	0.0419260151399	0.273295385252	0.00979520754113	0.183729286521	23.8416217169	-37.4148931868	-24.7109892901
6	1.19660380226	-0.197123006691	0.325617026097	0.226728688335	-0.293730733352	1.23913189508	-0.00461558540815	-0.0936451291491	-0.105206680685	-0.0259606548928	-0.037936955794	0.00361091250704	0.0413773349862	0.016615015608	0.0264680284782	0.196904086885	-0.00110387852035	0.0352103486825	0.258665510439	-0.00299588717227	0.232404797219	31.5175422063	-39.7460433309	-42.8619308212
7	1.03309133662	-1.0438836347	-0.384035034723	2.39125627461	0.101978042767	0.59014145727	-0.0471570575202	0.108055958226	-0.165458918508	-0.181497584545	0.0494622861901	0.369958104427	-0.0366275196041	-0.178661515315	-0.0243290284229	0.150160564283	-0.0438316298822	-0.0125608468816	0.287204566633	0.0134302593116	0.206307067234	10.6066130326	-33.1033831273	-55.400256904
8	1.02686284915	-0.398700199862	0.743144794208	0.761319407443	-0.619676619282	2.34012647853	0.0653610397997	0.0318977225693	-0.0817945324624	-0.0286188559447	-0.0974420298243	-0.0833561707119	0.274300978222	0.252079535715	0.0389189610749	0.173940570395	-0.00380368680985	0.0296370556211	0.226279276052	-0.00908930978984	0.188948150889	29.9152082169	-43.1608062954	-47.3238544636
9	3.18141056358	1.27280199466	-0.520486479658	1.17966260419	0.0887743162827	2.51767873136	-0.0611471168906	0.232316040677	0.279287429292	-0.0710123096847	0.0944517773709	0.161232697138	0.0400086813476	-0.101259037517	-0.0337583996554	0.253904937522	0.0436402126313	-0.0432505975979	0.214407589374	0.0097570361954	0.251197555648	-4.54960267863	-4.18630173498	3.13651919261
10	1.21895040663	-0.323962931386	0.0525067869144	0.184239763169	-0.0661766615925	1.19442046773	-0.011555167748	0.0913079529445	0.00585097751802	0.0124606641953	-0.0258620241704	0.0220569055963	0.00608035444032	0.0122918371903	0.0283402753893	0.247384463401	0.0115661078788	-0.0214055879705	0.182889079279	-0.0362809804499	0.270154860217	6.45920825113	-2.23888296834	16.7110899159
11	0.957956943656	1.19463916973	0.360158528218	2.65127964351	-0.471644036471	0.862783561924	-0.0365786852203	-0.421287742747	0.148920026936	0.0819114181991	-0.0236928352371	0.311070330441	-0.145564487421	-0.363273083815	0.0580846456476	0.283867232052	0.118491057029	0.0333626257171	0.344470871326	-0.0374872958601	0.282065893277	-14.7652136708	-8.53461834859	32.9644995993
12	1.64002764522	0.615564256187	-0.578303891368	1.68186350746	-0.975771425566	1.46507894698	-0.112120554317	-0.264734317679	0.198639701093	0.19160031603	0.144144750312	-0.140401649705	-0.165879147903	0.0228356718567	-0.0303610173646	0.257854061461	0.0802024930476	-0.0716368207277	0.271360426314	-0.0857321705185	0.321642211348	4.51021790065	1.54066171058	25.1183153872
13	3.44239342943	-1.23532251072	-0.5883458925	0.842049820129	-0.213496120125	3.10338155452	-0.0140635621926	-0.30269902097	0.136271780332	0.00122866667724	0.0832171345029	-0.0669454612332	0.0391643733071	0.0892592051653	-0.0737220121351	0.290053521102	-0.0732975929867	-0.064462077493	0.195301724912	0.00490947968677	0.239395411845	38.9875163052	-1.96862712909	-20.6636931218
14	1.45294543786	-0.207551198096	-0.0351506241538	0.230075634814	0.167282634053	0.810451637483	-0.0852230073524	0.0726346602042	0.134313285706	-0.0407922864734	0.0338740016791	0.0231784291282	-0.0719468606419	-0.0918022492718	0.0523786108848	0.270632677894	-0.0461899546695	-0.0431755167184	0.320525185299	0.0311013955383	0.381663066698	30.1160561257	3.97082590216	-37.1293646736
15	1.05908229542	-1.04225866667	-0.281152497794	2.53989871188	0.619460521277	1.10284501695	0.00507268091553	0.423874920455	0.256874223528	-0.175404928291	-0.0839905834816	-0.455804285039	-0.141853793026	0.203387411377	0.0778875867807	0.28679270534	-0.102624979656	0.0151480023227	0.487715162205	0.0493880411537	0.345992738098	51.3256436999	0.15120799543	-51.63558543
16	1.64757609516	-0.297632767342	-0.649642644165	0.833788635545	0.562729481297	1.64715875027	-0.00646488864095	0.335524124732	0.273172997864	-0.114512429751	0.0503233245511	0.0782733744504	-0.186912509664	-0.105198378748	-0.0477080265022	0.261161827568	-0.0339344782626	-0.0878204460509	0.367150789255	0.0922713083104	0.399308230017	32.0423235807	8.4469269049	-41.8768417164

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 136 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 137 through 274 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 275 through 341 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 342 through 471 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1 through 136 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 137 through 274 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 275 through 341 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 342 through 471 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 1 through 103 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 104 through 274 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 275 through 341 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 342 through 471 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 1 through 125 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 126 through 274 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 275 through 341 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 342 through 471 )

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