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- PDB-5kor: Arabidopsis thaliana fucosyltransferase 1 (FUT1) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5kor
TitleArabidopsis thaliana fucosyltransferase 1 (FUT1) in complex with GDP and a xylo-oligossacharide
ComponentsGalactoside 2-alpha-L-fucosyltransferase
KeywordsTRANSFERASE / fucosyltransferase / complex / XLLG
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
Xyloglucan fucosyltransferase / Xyloglucan fucosyltransferase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Galactoside 2-alpha-L-fucosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRocha, J. / de Sanctis, D. / Breton, C.
Funding support France, 1items
OrganizationGrant numberCountry
Univ. Grenoble Alpes France
CitationJournal: 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
DepositionJul 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Oct 10, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation_author / entity / entity_src_gen
Item: _citation_author.identifier_ORCID / _entity.formula_weight ..._citation_author.identifier_ORCID / _entity.formula_weight / _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
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)243,08327
Polymers237,5614
Non-polymers5,52323
Water10,917606
1
A: Galactoside 2-alpha-L-fucosyltransferase
B: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,40011
Polymers118,7802
Non-polymers2,6199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Galactoside 2-alpha-L-fucosyltransferase
D: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,68416
Polymers118,7802
Non-polymers2,90314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.975, 85.806, 150.723
Angle α, β, γ (deg.)90.00, 96.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#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: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-[beta-D-galactopyranose-(1-2)-alpha-D-xylopyranose-(1-6)]beta-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1387.204 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-1-2-2-3-2-3/a4-b1_b4-c1_b6-h1_c4-d1_c6-f1_d6-e1_f2-g1_h2-i1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(6+1)][a-D-Xylp]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 627 molecules

#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 606 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87257 Å / Relative weight: 1
ReflectionResolution: 2.2→49.28 Å / Num. obs: 113138 / % possible obs: 99.8 % / Redundancy: 4.4 % / Rsym value: 0.106 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.554 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KOP

5kop


Resolution: 2.2→39.678 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 22.73
RfactorNum. reflection% reflection
Rfree0.2149 11116 5.01 %
Rwork0.179 --
obs0.1807 113088 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14476 0 359 606 15441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115379
X-RAY DIFFRACTIONf_angle_d1.09720900
X-RAY DIFFRACTIONf_dihedral_angle_d15.9089094
X-RAY DIFFRACTIONf_chiral_restr0.1712261
X-RAY DIFFRACTIONf_plane_restr0.0072598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2250.28964080.27226855X-RAY DIFFRACTION100
2.225-2.25120.29873550.26517126X-RAY DIFFRACTION100
2.2512-2.27860.32944050.25356966X-RAY DIFFRACTION100
2.2786-2.30750.28943900.25447017X-RAY DIFFRACTION100
2.3075-2.33780.31293750.25436943X-RAY DIFFRACTION100
2.3378-2.36990.2783760.24617097X-RAY DIFFRACTION100
2.3699-2.40370.27884270.2396986X-RAY DIFFRACTION100
2.4037-2.43960.27973700.23787041X-RAY DIFFRACTION100
2.4396-2.47770.28813660.22966998X-RAY DIFFRACTION100
2.4777-2.51830.25133320.22537122X-RAY DIFFRACTION100
2.5183-2.56170.23983750.21586961X-RAY DIFFRACTION100
2.5617-2.60830.25863930.21447075X-RAY DIFFRACTION100
2.6083-2.65850.24183490.21637014X-RAY DIFFRACTION100
2.6585-2.71270.24383960.21216967X-RAY DIFFRACTION100
2.7127-2.77170.24384060.2097041X-RAY DIFFRACTION100
2.7717-2.83610.25073690.20577095X-RAY DIFFRACTION100
2.8361-2.9070.24974210.20396889X-RAY DIFFRACTION100
2.907-2.98560.22433800.18877054X-RAY DIFFRACTION100
2.9856-3.07340.22323270.18747130X-RAY DIFFRACTION100
3.0734-3.17260.20643470.18067034X-RAY DIFFRACTION100
3.1726-3.28590.22143520.18017021X-RAY DIFFRACTION100
3.2859-3.41740.22693760.16857071X-RAY DIFFRACTION100
3.4174-3.57290.19623560.15857022X-RAY DIFFRACTION100
3.5729-3.76110.20343150.15397070X-RAY DIFFRACTION100
3.7611-3.99650.1543970.13797028X-RAY DIFFRACTION100
3.9965-4.30480.16913310.12977078X-RAY DIFFRACTION100
4.3048-4.73740.15783650.13097035X-RAY DIFFRACTION100
4.7374-5.42140.16523680.13887040X-RAY DIFFRACTION100
5.4214-6.82470.19633600.16057041X-RAY DIFFRACTION100
6.8247-39.68410.17143290.1587040X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.2245-0.0444-0.31090.91360.22973.09260.0339-0.21520.14690.03430.0265-0.066-0.00650.40860.00370.26350.04370.01720.2442-0.01180.22755.4786-22.960178.281
22.8465-0.46070.74590.3212-0.03491.7950.07790.29370.134-0.093-0.06950.02720.07560.1192-0.00190.28180.0340.02240.1864-0.01460.2692-7.5069-25.601254.6166
32.55990.28490.79111.72240.02091.9314-0.02310.3740.0338-0.20750.01990.03230.0561-0.09680.00360.2522-0.08030.01620.2435-0.03720.2447-57.5172-21.955928.7778
42.85660.05551.13030.38890.00751.72420.0006-0.35170.17740.0536-0.0362-0.0401-0.0236-0.0904-0.00940.2575-0.06210.01210.2209-0.03690.25-44.1375-18.869152.7633
51.85760.685-0.12211.3050.07311.65640.1689-0.1626-0.07940.2298-0.0794-0.0918-0.03630.12140.00460.2494-0.0318-0.01750.16650.0250.21214.973226.974947.0062
62.53950.59890.77460.48070.28681.0208-0.00220.38220.0323-0.05320.06520.0053-0.05270.02390.00080.2264-0.01310.01720.2261-0.0140.2197-7.913224.320922.963
72.65430.42070.06651.17460.1312.63870.06640.65140.0699-0.1555-0.00110.0704-0.0892-0.24420.00010.251-0.0056-0.00250.3891-0.0390.2512-57.714814.7996-1.6079
83.22490.4370.82860.47790.11011.46380.0877-0.32930.12630.0807-0.1090.0166-0.059-0.11110.00070.2421-0.05040.01240.2251-0.03140.2428-44.662417.280922.587
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 92 through 323 )
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 558 )
3X-RAY DIFFRACTION3chain 'B' and (resid 95 through 323 )
4X-RAY DIFFRACTION4chain 'B' and (resid 324 through 558 )
5X-RAY DIFFRACTION5chain 'C' and (resid 94 through 323 )
6X-RAY DIFFRACTION6chain 'C' and (resid 324 through 558 )
7X-RAY DIFFRACTION7chain 'D' and (resid 94 through 323 )
8X-RAY DIFFRACTION8chain 'D' and (resid 324 through 558 )

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