PDB-6su7: Complex between a UDP-glucosyltransferase from Polygonum tinctori...

ID or keywords:

Entry

Database: PDB / ID: 6su7

Title

Complex between a UDP-glucosyltransferase from Polygonum tinctorium capable of glucosylating indoxyl and 3,4-Dichloroaniline

Components

Glycosyltransferase

Keywords

TRANSFERASE / 3 / 4-Dichloroaniline GT-B Glucosyltransferase Indigo

Function / homology

UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase /

Transferases; Glycosyltransferases; Hexosyltransferases / 3,4-Dichloroaniline /

Glycosyltransferase

Function and homology information

Biological species

Persicaria tinctoria (plant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Fredslund, F. / Teze, D. / Svensson, B. / Adams, P.D. / Welner, D.H.

Funding support

Denmark, 2items

Citation

Journal: Acs Catalysis / Year: 2021
Title: O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering
Authors: Teze, D. / Coines, J. / Fredslund, F. / Dubey, K.D. / Bidart, G.N. / Adams, P.D. / Dueber, J.E. / Svensson, B. / Rovira, C. / Welner, D.H.

History

Deposition	Sep 13, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 30, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 21, 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	6su7.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb6su7.ent.gz	861.6 KB	Display	PDB format
PDBx/mmJSON format	6su7.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/su/6su7 ftp://data.pdbj.org/pub/pdb/validation_reports/su/6su7	HTTPS FTP

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Related structure data

Related structure data	6su6C 5nlmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2oa8-d 5hjp-2 5nlm-1 5kyj-2 6bzi-3 1uhl-d 2qmc-3 6k9m-1 5kya-1 2ipi-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

6su6C

5nlmS

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glycosyltransferase

B: Glycosyltransferase

C: Glycosyltransferase

D: Glycosyltransferase

hetero molecules

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

1

A: Glycosyltransferase

hetero molecules

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

2

B: Glycosyltransferase

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

3

C: Glycosyltransferase

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

4

D: Glycosyltransferase

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

Unit cell

Length a, b, c (Å)	93.353, 119.362, 170.626
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	THR	THR	LEU	LEU	(chain 'A' and (resid 10 through 102 or resid 104 through 476))	A	A	10 - 102	32 - 124
1	2	1	ASP	ASP	ASP	ASP	(chain 'A' and (resid 10 through 102 or resid 104 through 476))	A	A	104 - 314	126 - 336
1	3	1	PRO	PRO	LYS	LYS	(chain 'A' and (resid 10 through 102 or resid 104 through 476))	A	A	330 - 476	352 - 498
2	4	1	THR	THR	LEU	LEU	(chain 'B' and (resid 10 through 102 or resid 104 through 476))	B	B	10 - 102	32 - 124
2	5	1	ASP	ASP	ASP	ASP	(chain 'B' and (resid 10 through 102 or resid 104 through 476))	B	B	104 - 314	126 - 336
2	6	1	PRO	PRO	LYS	LYS	(chain 'B' and (resid 10 through 102 or resid 104 through 476))	B	B	330 - 476	352 - 498
1	7	2	THR	THR	ALA	ALA	(chain 'C' and (resid 9 through 251 or resid 261 through 476))	C	C	9 - 250	31 - 272
1	8	2	PRO	PRO	ASP	ASP	(chain 'C' and (resid 9 through 251 or resid 261 through 476))	C	C	261 - 314	283 - 336
1	9	2	PRO	PRO	LYS	LYS	(chain 'C' and (resid 9 through 251 or resid 261 through 476))	C	C	330 - 476	352 - 498
2	10	2	THR	THR	ALA	ALA	chain 'D'	D	D	9 - 250	31 - 272
2	11	2	PRO	PRO	ASP	ASP	chain 'D'	D	D	261 - 314	283 - 336
2	12	2	PRO	PRO	LYS	LYS	chain 'D'	D	D	330 - 476	352 - 498

NCS ensembles :

ID
1
2

#1: Protein	Glycosyltransferase / Mass: 54522.129 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Persicaria tinctoria (plant) / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A2R2JFJ4, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical	ChemComp-LV5 / 3,4-Dichloroaniline / Dichloroaniline Mass: 162.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₅Cl₂N / Feature type: SUBJECT OF INVESTIGATION
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: 2.18 Å³/Da / Density % sol: 43.56 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2M MGCL2, 0.1M HEPES pH 7.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
Detector	Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 2, 2018
Radiation	Monochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9677 Å / Relative weight: 1
Reflection	Resolution: 2.75→50.28 Å / Num. obs: 50246 / % possible obs: 99.29 % / Observed criterion σ(F): 0 / Redundancy: 5.3 % / B_iso Wilson estimate: 62.47 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.1523 / R_pim(I) all: 0.07272 / Net I/σ(I): 5.1
Reflection shell	Resolution: 2.75→2.84 Å / Redundancy: 5.5 % / R_merge(I) obs: 0.824 / Mean I/σ(I) obs: 1.27 / Num. unique obs: 4826 / CC_1/2: 0.538 / R_pim(I) all: 0.3816 / % possible all: 97.08

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Processing

Software

Name	Version	Classification
PHENIX	1.16_3549	refinement
PHENIX	1.16_3549	refinement
xia2	0.5.5	data reduction
xia2	0.5.5	data scaling
PHASER		phasing
DIALS	1.9.3	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5NLM

5nlm

Resolution: 2.75→50.28 Å / SU ML: 0.4571 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 34.6686

	R_factor	Num. reflection	% reflection
R_free	0.2873	2471	4.93 %
R_work	0.2562	-	-
obs	0.2578	50132	99.31 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 91.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→50.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13803	0	9	0	13812

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14155
X-RAY DIFFRACTION	f_angle_d	0.5313	19234
X-RAY DIFFRACTION	f_chiral_restr	0.041	2175
X-RAY DIFFRACTION	f_plane_restr	0.0037	2491
X-RAY DIFFRACTION	f_dihedral_angle_d	10.3343	8573

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 (%)
2.75-2.8	0.3861	126	0.3844	2460	X-RAY DIFFRACTION	94.83
2.8-2.86	0.3596	127	0.3656	2665	X-RAY DIFFRACTION	99.86
2.86-2.92	0.3759	151	0.3422	2614	X-RAY DIFFRACTION	99.89
2.92-2.99	0.3241	137	0.325	2623	X-RAY DIFFRACTION	99.93
2.99-3.06	0.3552	141	0.3215	2615	X-RAY DIFFRACTION	99.96
3.06-3.14	0.3564	143	0.3324	2633	X-RAY DIFFRACTION	99.89
3.14-3.24	0.3565	143	0.322	2635	X-RAY DIFFRACTION	99.78
3.24-3.34	0.3691	147	0.3261	2620	X-RAY DIFFRACTION	99.93
3.34-3.46	0.3498	131	0.3143	2660	X-RAY DIFFRACTION	99.79
3.46-3.6	0.2955	129	0.2713	2654	X-RAY DIFFRACTION	99.93
3.6-3.76	0.3401	151	0.255	2614	X-RAY DIFFRACTION	99.78
3.76-3.96	0.2825	136	0.2434	2661	X-RAY DIFFRACTION	99.86
3.96-4.21	0.2309	125	0.2302	2660	X-RAY DIFFRACTION	99.54
4.21-4.53	0.2405	135	0.1932	2679	X-RAY DIFFRACTION	99.79
4.53-4.99	0.211	134	0.1948	2619	X-RAY DIFFRACTION	97.35
4.99-5.71	0.2533	132	0.2159	2720	X-RAY DIFFRACTION	100
5.71-7.19	0.2842	126	0.2574	2754	X-RAY DIFFRACTION	100
7.19-50.28	0.2651	157	0.2292	2775	X-RAY DIFFRACTION	97.57

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	2.57692200555	0.380661670956	1.25767928586	3.16832956447	-1.41493161057	2.47129910834	-0.0482511703903	-1.17713169482	0.630480729176	0.294897508919	-0.409525324761	0.14973583836	0.493876067511	-1.42034376844	0.164490487765	1.73881378596	0.155534464297	0.246604509935	0.826073394417	-0.365748258208	0.36807365582	102.469738486	14.1054542897	94.848741529
2	2.71938421748	-0.150208071226	-0.193982832839	3.64683580141	4.02339321616	5.52979761217	0.256449059692	-0.449051057408	0.369256374982	-0.0211926133447	-0.0981067190838	-0.123563040932	-0.648511188307	0.103074707902	-0.189865303673	0.525879446524	-0.0952292603081	0.146452682309	0.356091375106	-0.0128505224042	0.370540127778	115.687005894	5.63363874421	84.1266894548
3	3.72950488643	-1.27733420093	2.45580471576	3.02676122189	-2.76127820125	4.63560847298	-0.158468957722	-0.763104751427	-0.158845025332	0.732533834077	0.233312974599	-0.551243793012	0.233287983868	1.51221277058	-0.121554814472	0.858197132196	0.364550407768	-0.0830397481316	1.43588855196	-0.232925352221	0.9077926968	65.7021595784	-11.2525900427	81.0591048324
4	2.41401225738	0.78447540664	2.42459182148	6.83437648841	3.61613235075	6.53576959724	-0.518203809542	0.141073541687	0.619466304008	0.792704221193	0.334948360883	-0.524705112927	-1.34119340468	1.21366259021	0.219661931774	1.3171609591	-0.226136997313	-0.187056442163	1.01354685756	-0.0627499003436	0.941439107671	64.2583046189	12.5733370889	87.8023571118
5	0.875134258247	-0.114531204073	0.108104038423	4.36094449267	0.641989412458	3.44998870489	0.131296181058	0.139143038854	0.0241956933806	-0.48895651762	-0.182402246987	0.0185144240191	-0.0897704062296	0.122504787659	0.0612119463107	0.150278564451	0.0274216050527	0.105656565472	0.273172449705	-0.0567527111261	0.389114237074	45.1471444244	2.03842040597	41.4023624657
6	4.00532841837	0.770111293688	-0.150094683235	5.06397536722	-0.801604808591	4.95261719498	-0.0942623225247	0.138772699721	0.204460004061	0.160622439033	-0.11887028608	-0.633958824399	-0.461743767107	0.353155335816	0.122525655575	0.332404896714	-0.0478932011381	-0.0353935426386	0.309739113331	0.018943737742	0.448835461644	51.137158227	27.0879891727	51.5203788608
7	2.61813764762	0.273332338666	0.0447039373973	6.41718939912	0.443627712406	1.22543507721	-0.110625332656	-0.348435280256	-0.139206583038	1.70015130433	-0.182843913757	0.597824609344	0.0756702009184	-0.433653890268	0.172926871065	0.350670852684	-0.0228979612796	0.283275959953	0.436686114437	-0.129662709452	0.559821820062	35.6538064472	8.12493321573	58.3729472646
8	7.4936865173	-2.56714575129	0.148870537539	7.35769747746	0.93318677817	8.36953509038	0.158155014301	-0.384384990343	-0.397142426155	0.988014078913	0.0954973176426	1.33697729064	0.265777486721	0.31924983082	-0.282524069189	0.297498180593	-0.139340392535	0.0383620261578	0.437537579599	-0.0809953428734	0.52964096205	96.3601688158	-8.22326049488	51.0728838399
9	3.09971501172	-1.96020736805	0.195777836278	5.36872605518	1.01190109652	4.71990910202	0.291999230976	0.141139081123	0.15633498355	-0.684464281611	-0.314354592435	0.423410533583	-0.613119469746	-0.332106800807	0.017608993551	0.375260136484	-0.00755098936114	0.0274178852284	0.454540106204	-0.0673171057028	0.468621463328	91.9863685549	-0.953829213828	36.2652161709
10	2.94987550174	0.990600467753	-1.27694848087	3.33097636374	-0.0562682476222	1.63900689768	-0.00679635046756	-0.306231274416	-0.354432082353	1.08553556686	-0.0168201749634	1.49934013498	0.167352337721	-0.797963753117	-0.126330690954	0.28098414332	-0.125881065153	0.0652696915257	0.485000384634	-0.104862290376	0.939149002104	85.1310618915	1.47672039567	52.1437899923
11	3.82612076552	0.417671747176	0.0269613624028	6.95711533719	-1.65172749329	5.83209553735	0.157100514811	0.402562344043	0.218094853916	0.355010962844	-0.464784127853	-0.921768646057	-0.0568941113934	0.302898737278	0.241099326742	0.542343727781	0.083107089739	-0.1340988398	0.441469391954	0.0531668468389	0.778819455551	99.8033496492	22.1086358853	52.7268404974
12	1.25210147366	0.115338290307	0.363675831568	9.08457437694	-0.967422671496	1.64735959882	-0.139576677508	-0.251162818741	-0.15116333684	1.27162856139	-0.0160781755423	0.564503193058	-0.461017360063	-0.6259506388	0.101366896587	0.429770449909	0.0913028694525	0.091016010382	0.682947706209	-0.0111402364633	0.644947109989	85.4285370708	14.2286073727	53.7843270575
13	3.1633186956	-0.3090933267	2.17860571139	2.48121455737	0.148467819551	2.53769263333	0.194030603197	-0.434438969931	-0.481855163802	0.334711832376	0.037179640167	0.265440510019	0.647502472462	-0.362158867434	-0.190775581812	0.768513006256	-0.206840965486	0.0945016636517	0.474143963449	0.0505016413904	0.527449559108	110.712519224	-16.5464566769	81.7718189334
14	2.96134284275	2.0737043729	0.614301456665	4.64847386385	0.164433152233	5.87558544435	0.371786924753	-0.637873491195	-0.0801637520165	-0.0591842912537	-0.193162484933	-0.92059481693	-0.225869540067	0.705897433834	-0.0496976405692	0.342046966886	-0.039872288729	0.127125955021	0.369487695072	-0.0274038267344	0.411854279853	120.901825458	-6.95509180287	75.4030327842

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 262 through 345 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 346 through 476 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 9 through 261 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 262 through 476 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 10 through 261 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 262 through 435 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 436 through 476 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 10 through 47 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 48 through 211 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 212 through 261 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 262 through 403 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 404 through 476 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 9 through 211 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 212 through 261 )

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi