PDB-6llz: Crystal Structure of Fagopyrum esculentum M UGT708C1 complexed wi...

ID or keywords:

Entry

Database: PDB / ID: 6llz

Title

Crystal Structure of Fagopyrum esculentum M UGT708C1 complexed with UDP-glucose

Components

UDP-glycosyltransferase 708C1

Keywords

TRANSFERASE / C-glycosides / C-glucosyltransferases / crystal structures / UDP-glucose

Function / homology

Function and homology information

2-hydroxyflavanone C-glucosyltransferase / 2-hydroxyflavanone C-glucosyltransferase activity / UDP-glucosyltransferase activity
Similarity search - Function

Biological species

Fagopyrum esculentum (common buckwheat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.006 Å

Authors

Wang, X. / Liu, M.

Funding support

China, 2items

Citation

Journal: Plant Cell / Year: 2020
Title: Crystal Structures of theC-Glycosyltransferase UGT708C1 from Buckwheat Provide Insights into the Mechanism ofC-Glycosylation.
Authors: Liu, M. / Wang, D. / Li, Y. / Li, X. / Zong, G. / Fei, S. / Yang, X. / Lin, J. / Wang, X. / Shen, Y.

History

Deposition	Dec 24, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 9, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2020	Group: Database references / Structure summary / Category: audit_author / citation / citation_author Item: _audit_author.identifier_ORCID / _audit_author.name ..._audit_author.identifier_ORCID / _audit_author.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Nov 22, 2023	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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PDBx/mmCIF format	6llz.cif.gz	357.9 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ll/6llz ftp://data.pdbj.org/pub/pdb/validation_reports/ll/6llz	HTTPS FTP

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Related structure data

Related structure data	6llgC 6llwC 2acvS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5aau-d 6yu6-2 7cyw-d 3os9-2 3pns-5 3isq-d 5ak2-d 6y87-5 6y87-1 5vdq-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) 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	#254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: UDP-glycosyltransferase 708C1

B: UDP-glycosyltransferase 708C1

hetero molecules

102 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: UDP-glycosyltransferase 708C1

hetero molecules

defined by author&software
Evidence: gel filtration
51 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: UDP-glycosyltransferase 708C1

hetero molecules

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

Unit cell

Length a, b, c (Å)	98.914, 143.757, 69.758
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-1249- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A
2	1	(chain B and (resid 18 through 255 or (resid 256...

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-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	ASP	ASP	LYS	LYS	chain A	A	A	18 - 456	18 - 456
2	1	ASP	ASP	ASN	ASN	(chain B and (resid 18 through 255 or (resid 256...	B	B	18 - 255	18 - 255
2	2	LYS	LYS	LYS	LYS	(chain B and (resid 18 through 255 or (resid 256...	B	B	256	256
2	3	ASP	ASP	LYS	LYS	(chain B and (resid 18 through 255 or (resid 256...	B	B	18 - 456	18 - 456
2	4	ASP	ASP	LYS	LYS	(chain B and (resid 18 through 255 or (resid 256...	B	B	18 - 456	18 - 456
2	5	ASP	ASP	LYS	LYS	(chain B and (resid 18 through 255 or (resid 256...	B	B	18 - 456	18 - 456
2	6	ASP	ASP	LYS	LYS	(chain B and (resid 18 through 255 or (resid 256...	B	B	18 - 456	18 - 456

#1: Protein	UDP-glycosyltransferase 708C1 / C-glucosyltransferase a / FeCGTa / UDP-glucose:2-hydroxyflavanone C-glucosyltransferase Mass: 50429.480 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fagopyrum esculentum (common buckwheat) Gene: UGT708C1 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0A1HA03, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 466 / 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: 2.46 Å³/Da / Density % sol: 49.97 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M ammonium sulfate, 0.1M MES pH 7.0, 26.5%(w/v) polyethylene glycol 5000, 26%(w/v) benzamidine hydrochloride, 5mM UDP-glucose

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL19U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 25, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.94→50.059 Å / Num. obs: 69452 / % possible obs: 94.4 % / Redundancy: 6.3 % / R_merge(I) obs: 0.089 / R_pim(I) all: 0.04 / R_rim(I) all: 0.098 / Χ²: 0.919 / Net I/σ(I): 9.5

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.94-1.97	2.7	0.363	239	0.943	0.218	0.427	0.564	6.6
1.97-2.01	6.3	0.269	3573	0.962	0.117	0.294	0.831	98.3
2.01-2.05	6.6	0.233	3627	0.967	0.099	0.254	0.857	99.2
2.05-2.09	6.6	0.214	3588	0.968	0.091	0.234	0.887	99.8
2.09-2.14	6.5	0.19	3629	0.974	0.082	0.207	0.9	99.7
2.14-2.18	6.5	0.175	3642	0.98	0.075	0.191	0.928	99.7
2.18-2.24	6.3	0.174	3634	0.976	0.076	0.191	1.22	99.6
2.24-2.3	6	0.153	3546	0.977	0.068	0.168	1.052	98.1
2.3-2.37	6.5	0.147	3638	0.982	0.063	0.16	1.016	99.9
2.37-2.44	6.6	0.136	3628	0.981	0.058	0.148	1.022	99.8
2.44-2.53	6.6	0.128	3672	0.983	0.055	0.14	1.016	99.8
2.53-2.63	6.5	0.117	3624	0.985	0.051	0.128	0.994	99.7
2.63-2.75	6.3	0.111	3646	0.985	0.049	0.122	0.985	98.6
2.75-2.9	6.2	0.103	3609	0.986	0.046	0.113	0.944	97.7
2.9-3.08	6.6	0.096	3636	0.99	0.041	0.105	0.895	99.7
3.08-3.32	6.4	0.088	3684	0.99	0.038	0.096	0.876	99.3
3.32-3.65	5.9	0.08	3625	0.991	0.036	0.088	0.832	97.6
3.65-4.18	6.2	0.074	3683	0.992	0.033	0.082	0.772	99.1
4.18-5.26	5.8	0.071	3706	0.993	0.033	0.079	0.717	98.1
5.26-50	5.7	0.068	3823	0.994	0.032	0.075	0.688	96.3

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Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ACV

2acv

Resolution: 2.006→50 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.69

	R_factor	Num. reflection	% reflection
R_free	0.2015	3385	5.08 %
R_work	0.1679	-	-
obs	0.1696	66610	98.92 %

Solvent computation

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

Displacement parameters

B_iso max: 125.9 Å² / B_iso mean: 35.9261 Å² / B_iso min: 15.43 Å²

Refinement step

Cycle: final / Resolution: 2.006→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6770	0	72	466	7308
B_iso mean	-	-	34.73	40.98	-
Num. residues	-	-	-	-	872

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7036
X-RAY DIFFRACTION	f_angle_d	1.191	9594
X-RAY DIFFRACTION	f_chiral_restr	0.082	1076
X-RAY DIFFRACTION	f_plane_restr	0.007	1224
X-RAY DIFFRACTION	f_dihedral_angle_d	6.087	4164

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3988	X-RAY DIFFRACTION	11.242	TORSIONAL
1	2	B	3988	X-RAY DIFFRACTION	11.242	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.0063-2.0349	0.2312	130	0.1892	2426	93
2.0349-2.0653	0.2322	139	0.1793	2646	100
2.0653-2.0976	0.2409	141	0.1701	2609	100
2.0976-2.132	0.2198	158	0.1677	2636	100
2.132-2.1687	0.2389	125	0.1738	2617	100
2.1687-2.2082	0.2067	131	0.1777	2630	100
2.2082-2.2506	0.2243	140	0.1686	2647	100
2.2506-2.2966	0.1957	156	0.1709	2540	98
2.2966-2.3465	0.2388	144	0.1785	2623	99
2.3465-2.4011	0.2243	151	0.1796	2636	100
2.4011-2.4611	0.2268	139	0.1755	2627	100
2.4611-2.5277	0.1796	158	0.1728	2616	100
2.5277-2.602	0.2265	154	0.1718	2644	100
2.602-2.686	0.2178	121	0.1755	2654	99
2.686-2.782	0.2404	123	0.1749	2605	98
2.782-2.8934	0.1891	119	0.1755	2631	98
2.8934-3.0251	0.2064	154	0.1755	2640	100
3.0251-3.1845	0.2283	142	0.1821	2671	100
3.1845-3.384	0.1846	133	0.1706	2654	100
3.384-3.6452	0.1958	147	0.1699	2633	98
3.6452-4.0119	0.1847	140	0.1566	2672	99
4.0119-4.5921	0.1433	146	0.1373	2686	99
4.5921-5.7842	0.2329	146	0.162	2663	97
5.7842-50	0.1854	148	0.1721	2819	98

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	1.1298	-0.4341	0.5859	1.9191	0.1209	2.0544	0.0178	0.0662	-0.0693	-0.0501	-0.0258	-0.0048	0.007	0.0326	0.0163	0.1848	-0.0392	0.0053	0.1675	0.0018	0.1688	25.2974	19.9156	-11.4121
2	2.2376	2.6365	-1.2085	4.9378	-2.0271	1.4727	0.0631	0.0804	0.1241	0.1184	-0.021	0.1954	-0.0542	-0.0189	-0.0517	0.2188	0.0341	-0.0429	0.2232	-0.0264	0.1371	22.7553	13.0549	5.114
3	1.1448	1.2674	-0.186	3.1977	0.1212	0.8175	-0.0079	0.0259	-0.2032	0.0793	-0.0816	-0.0723	0.1005	-0.0201	0.0916	0.2499	0.0039	-0.042	0.2147	-0.0141	0.1822	22.2731	1.4163	4.1273
4	1.3446	0.2945	0.4324	1.6915	0.0891	2.9131	0.0619	0.0051	-0.0889	0.0761	0.0383	-0.1943	-0.1422	0.0736	-0.0744	0.1462	0.0097	0.0112	0.134	-0.0017	0.186	-12.1001	35.6598	-21.3182
5	0.3061	-0.106	-0.182	3.6019	0.7104	1.1083	-0.0131	-0.0758	-0.0628	-0.0369	0.0766	-0.2328	0.0276	0.1323	-0.0398	0.1669	0.005	-0.0111	0.2329	0.0146	0.1884	-12.3081	18.929	-37.3412

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 18 through 224 )	A	18 - 224
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 225 through 276 )	A	225 - 276
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 277 through 456 )	A	277 - 456
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 18 through 224 )	B	18 - 224
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 225 through 456 )	B	225 - 456

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