PDB-5kop: Arabidopsis thaliana fucosyltransferase 1 (FUT1) in its apo-form

ID or keywords:

Entry

Database: PDB / ID: 5kop

Title

Arabidopsis thaliana fucosyltransferase 1 (FUT1) in its apo-form

Components

Galactoside 2-alpha-L-fucosyltransferase

Keywords

TRANSFERASE /

fucosyltransferase / apo-form / Golgi

Function / homology

Function and homology information

galactoside 2-alpha-L-fucosyltransferase activity / xyloglucan biosynthetic process /

fucosyltransferase activity / cell wall biogenesis /

Transferases; Glycosyltransferases; Hexosyltransferases / Golgi cisterna membrane / Golgi medial cisterna / cell wall organization /

Golgi membrane /

Golgi apparatus / protein homodimerization activity
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Rocha, J. / de Sanctis, D. / Breton, C.

Funding support

France, 1items

Citation

Journal: Plant Cell / Year: 2016
Title: Structure of Arabidopsis thaliana FUT1 Reveals a Variant of the GT-B Class Fold and Provides Insight into Xyloglucan Fucosylation.
Authors: Rocha, J. / Ciceron, F. / de Sanctis, D. / Lelimousin, M. / Chazalet, V. / Lerouxel, O. / Breton, C.

History

Deposition	Jul 1, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 12, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 23, 2016	Group: Database references
Revision 1.2	Oct 24, 2018	Group: Data collection / Source and taxonomy / Category: entity_src_gen Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_vector

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5kop.cif.gz	742.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ko/5kop ftp://data.pdbj.org/pub/pdb/validation_reports/ko/5kop	HTTPS FTP

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Related structure data

Related structure data	5korC C: citing same article (ref.)
Similar structure data	2vd5-1 5glf-d 6ss2-d 4w8w-d 4ydj-2 4idj-d 6p1j-1 3ivk-2 4j0j-d 1nca-d 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

Deposited unit

A: Galactoside 2-alpha-L-fucosyltransferase

B: Galactoside 2-alpha-L-fucosyltransferase

C: Galactoside 2-alpha-L-fucosyltransferase

D: Galactoside 2-alpha-L-fucosyltransferase

hetero molecules

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

1

A: Galactoside 2-alpha-L-fucosyltransferase

B: Galactoside 2-alpha-L-fucosyltransferase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Galactoside 2-alpha-L-fucosyltransferase

D: Galactoside 2-alpha-L-fucosyltransferase

hetero molecules

defined by author&software
119 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	87.838, 85.863, 150.467
Angle α, β, γ (deg.)	90.00, 96.22, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Galactoside 2-alpha-L-fucosyltransferase / / Xyloglucan alpha-(1 / 2)-fucosyltransferase / AtFUT1 Mass: 59390.199 Da / Num. of mol.: 4 / Fragment: UNP Residues 69-558 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FUT1, FT1, MUR2, At2g03220, T18E12.11 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9SWH5, EC: 2.4.1.69
#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.2 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, PEG 8000, sodium chloride / PH range: 7.2-7.8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 2.1→49.24 Å / Num. obs: 129318 / % possible obs: 99.6 % / Redundancy: 4.2 % / R_sym value: 0.075 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.9 / R_sym value: 0.598 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1→43.66 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.98

	R_factor	Num. reflection	% reflection
R_free	0.2151	12683	4.99 %
R_work	0.1773	-	-
obs	0.1792	129254	99.57 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→43.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14516	0	25	655	15196

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	15139
X-RAY DIFFRACTION	f_angle_d	1.368	20566
X-RAY DIFFRACTION	f_dihedral_angle_d	15.764	8978
X-RAY DIFFRACTION	f_chiral_restr	0.239	2185
X-RAY DIFFRACTION	f_plane_restr	0.01	2623

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 (%)
2.1-2.1239	0.3286	443	0.2924	8014	X-RAY DIFFRACTION	99
2.1239-2.1489	0.3312	468	0.2859	8094	X-RAY DIFFRACTION	100
2.1489-2.1751	0.317	427	0.2731	7907	X-RAY DIFFRACTION	99
2.1751-2.2026	0.3027	428	0.2629	8067	X-RAY DIFFRACTION	99
2.2026-2.2316	0.3054	425	0.2574	7978	X-RAY DIFFRACTION	99
2.2316-2.2621	0.3071	405	0.2497	8007	X-RAY DIFFRACTION	99
2.2621-2.2945	0.2626	463	0.2356	7972	X-RAY DIFFRACTION	100
2.2945-2.3287	0.291	456	0.2315	8105	X-RAY DIFFRACTION	100
2.3287-2.3651	0.2903	444	0.2269	8028	X-RAY DIFFRACTION	100
2.3651-2.4039	0.28	418	0.2254	8030	X-RAY DIFFRACTION	100
2.4039-2.4453	0.2916	468	0.213	8029	X-RAY DIFFRACTION	100
2.4453-2.4898	0.2537	388	0.2191	7952	X-RAY DIFFRACTION	100
2.4898-2.5377	0.248	390	0.2063	8148	X-RAY DIFFRACTION	100
2.5377-2.5894	0.2692	343	0.2065	8164	X-RAY DIFFRACTION	100
2.5894-2.6457	0.2482	450	0.2016	7990	X-RAY DIFFRACTION	100
2.6457-2.7073	0.2182	437	0.1962	8042	X-RAY DIFFRACTION	99
2.7073-2.775	0.2621	419	0.2006	8010	X-RAY DIFFRACTION	99
2.775-2.85	0.2515	418	0.195	8084	X-RAY DIFFRACTION	100
2.85-2.9338	0.2648	396	0.1888	8145	X-RAY DIFFRACTION	100
2.9338-3.0285	0.208	407	0.1902	8017	X-RAY DIFFRACTION	100
3.0285-3.1367	0.2239	412	0.1879	8073	X-RAY DIFFRACTION	100
3.1367-3.2623	0.22	437	0.1798	8082	X-RAY DIFFRACTION	100
3.2623-3.4107	0.2144	419	0.1723	8019	X-RAY DIFFRACTION	100
3.4107-3.5904	0.2086	463	0.1616	7998	X-RAY DIFFRACTION	99
3.5904-3.8153	0.1815	397	0.1507	8078	X-RAY DIFFRACTION	100
3.8153-4.1096	0.1479	393	0.1302	8122	X-RAY DIFFRACTION	100
4.1096-4.5228	0.1609	371	0.1225	8099	X-RAY DIFFRACTION	100
4.5228-5.1764	0.1596	496	0.1278	7965	X-RAY DIFFRACTION	99
5.1764-6.5182	0.1817	423	0.1461	8039	X-RAY DIFFRACTION	100
6.5182-43.6698	0.1626	379	0.1605	8089	X-RAY DIFFRACTION	99

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	1.7624	0.4562	0.565	1.7915	-0.4788	0.1416	-0.043	-0.0747	-0.5202	-0.1156	0.1272	0.259	0.4394	-0.1699	0.0351	0.4105	-0.0072	0.0042	0.2735	0.0403	0.3347	-11.4086	-40.8302	77.1538
2	2.0962	-0.0598	-0.5272	0.7351	0.0002	2.4495	0.0681	-0.2989	0.2056	0.0942	-0.0112	-0.1181	-0.1615	0.5325	-0.0509	0.2335	0.001	0.0124	0.3294	-0.0312	0.2273	8.4898	-20.1463	78.8479
3	2.4872	-0.2753	0.559	0.3336	0.0903	1.3025	0.0902	0.3815	0.1045	-0.0959	-0.0796	0.0156	-0.0014	0.127	-0.0144	0.254	0.0465	0.0191	0.2412	0.0023	0.2349	-7.3261	-25.6468	54.133
4	2.9684	0.1264	0.7289	1.4871	-0.0196	2.1176	0.0051	0.4796	-0.0386	-0.1854	0.0134	0.0376	0.0898	0.0024	-0.0197	0.2223	-0.0509	0.0029	0.2468	-0.0255	0.2112	-57.3081	-21.9739	28.679
5	3.1748	-0.0885	1.3177	0.5318	-0.0571	1.796	-0.0282	-0.308	0.2127	0.0578	-0.0078	-0.0594	-0.0838	-0.0895	0.0213	0.2154	-0.0312	0.0211	0.1843	-0.0175	0.2207	-44.5505	-19.1106	52.8416
6	1.8248	0.4328	-0.0921	1.2809	-0.0902	1.8917	0.1384	-0.1038	-0.0751	0.2196	-0.0695	-0.0963	-0.0375	0.123	-0.0648	0.1953	-0.0091	-0.0131	0.1565	0.0158	0.1818	4.8394	26.6191	46.5525
7	2.968	0.8981	0.4666	0.8358	0.1362	1.0158	-0.0278	0.4938	0.0367	-0.0912	0.0955	0.0119	-0.0952	0.0148	-0.0569	0.1843	0.0084	0.0173	0.2775	-0.0056	0.1861	-8.2464	24.6116	21.8608
8	0.0291	-0.2487	-0.3649	0.3548	0.9452	1.5714	0.0882	0.2722	-0.5744	-0.0369	0.0329	-0.1494	0.3124	0.3214	-0.0338	0.4144	0.0476	-0.0625	0.4625	-0.1931	0.5862	-41.1685	-1.2711	3.2768
9	3.2773	0.2364	0.3385	1.3237	0.0089	3.052	0.0204	0.9359	0.1301	-0.2893	0.0092	0.1295	-0.1091	-0.2545	-0.0281	0.2488	-0.0004	-0.0183	0.514	0.0165	0.2462	-60.4626	17.3988	-2.7021
10	3.8596	0.3863	0.9781	0.5473	0.1017	1.6427	0.0852	-0.3555	0.1153	0.091	-0.0767	-0.004	-0.0669	-0.0857	-0.013	0.2022	-0.0342	0.017	0.1998	-0.0242	0.2049	-44.7561	16.88	22.9054

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 81 through 129 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 130 through 323 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 324 through 558 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 95 through 323 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 324 through 558 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 94 through 339 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 340 through 558 )
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 84 through 129 )
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 130 through 323 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 324 through 558 )

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