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- PDB-5koe: The structure of Arabidopsis thaliana FUT1 in complex with XXLG -

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Basic information

Entry
Database: PDB / ID: 5koe
TitleThe structure of Arabidopsis thaliana FUT1 in complex with XXLG
ComponentsGalactoside 2-alpha-L-fucosyltransferase
KeywordsCELL ADHESION / acetyl transferase / XXLG / GT37 / Arabidopsis thaliana
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
: / Galactoside 2-alpha-L-fucosyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.79 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
CitationJournal: Plant J. / Year: 2017
Title: Structural, mutagenic and in silico studies of xyloglucan fucosylation in Arabidopsis thaliana suggest a water-mediated mechanism.
Authors: Urbanowicz, B.R. / Bharadwaj, V.S. / Alahuhta, M. / Pena, M.J. / Lunin, V.V. / Bomble, Y.J. / Wang, S. / Yang, J.Y. / Tuomivaara, S.T. / Himmel, M.E. / Moremen, K.W. / York, W.S. / Crowley, M.F.
History
DepositionJun 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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 / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)220,45242
Polymers216,8944
Non-polymers3,55838
Water37,4172077
1
A: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,26315
Polymers54,2231
Non-polymers2,03914
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4437
Polymers54,2231
Non-polymers2206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,02712
Polymers54,2231
Non-polymers80411
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7188
Polymers54,2231
Non-polymers4957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules

D: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,98123
Polymers108,4472
Non-polymers2,53421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area8620 Å2
ΔGint-86 kcal/mol
Surface area36260 Å2
MethodPISA
6
C: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules

B: Galactoside 2-alpha-L-fucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,47119
Polymers108,4472
Non-polymers1,02417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6340 Å2
ΔGint-83 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.748, 80.150, 157.616
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 5 molecules ABCD

#1: Protein
Galactoside 2-alpha-L-fucosyltransferase / / Xyloglucan alpha-(1 / 2)-fucosyltransferase / AtFUT1


Mass: 54223.488 Da / Num. of mol.: 4 / Fragment: residues 84-558
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): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q9SWH5, EC: 2.4.1.69
#2: Polysaccharide alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[alpha-D-xylopyranose-(1-6)]beta-D- ...alpha-D-xylopyranose-(1-6)-beta-D-glucopyranose-(1-4)-[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: 1225.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DXylpa1-6DGlcpb1-4[DXylpa1-6]DGlcpb1-4[DGalpb1-2DXylpa1-6]DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5][a212h-1a_1-5][a2112h-1b_1-5]/1-1-1-1-2-2-2-3/a4-b1_b4-c1_b6-g1_c4-d1_c6-f1_d6-e1_g2-h1WURCSPDB2Glycan 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]{}}[(6+1)][a-D-Xylp]{[(2+1)][b-D-Galp]{}}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 2114 molecules

#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2077 / 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: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 7 mg/mL protein in 0.1 M MES pH 6.0 to 7.0 and 16% to 23% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54188 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Oct 13, 2014 / Details: Helios mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54188 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 191803 / % possible obs: 99.8 % / Redundancy: 7.75 % / Rmerge(I) obs: 0.0948 / Net I/σ(I): 11.61
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 5.32 % / Rmerge(I) obs: 0.7225 / Mean I/σ(I) obs: 1.48 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
PROTEUM PLUSdata collection
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.79→157.53 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.549 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21676 9305 4.9 %RANDOM
Rwork0.16564 ---
obs0.16811 182014 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å2-0 Å2-0.57 Å2
2--0.47 Å2-0 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.79→157.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14440 0 194 2077 16711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.01915732
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214453
X-RAY DIFFRACTIONr_angle_refined_deg2.0851.94421447
X-RAY DIFFRACTIONr_angle_other_deg1.0893.00333477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.02151930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8923.912708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.418152575
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9661569
X-RAY DIFFRACTIONr_chiral_restr0.1490.22284
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.02117789
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023684
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5241.2477579
X-RAY DIFFRACTIONr_mcbond_other1.5231.2477578
X-RAY DIFFRACTIONr_mcangle_it2.551.8569556
X-RAY DIFFRACTIONr_mcangle_other2.551.8569557
X-RAY DIFFRACTIONr_scbond_it1.9691.4598153
X-RAY DIFFRACTIONr_scbond_other1.9691.4598153
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1292.10611892
X-RAY DIFFRACTIONr_long_range_B_refined6.73116.33418716
X-RAY DIFFRACTIONr_long_range_B_other6.54515.418196
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.788→1.835 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 726 -
Rwork0.316 12867 -
obs--96.23 %
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)
10.8497-0.19660.21840.6986-0.15590.879-0.0520.0130.03330.001-0.0155-0.0602-0.00420.06230.06750.1083-0.00830.03760.07150.00870.023437.9533.274143.91
21.0965-0.08940.76880.2598-0.16810.8089-0.0471-0.1507-0.0447-0.00330.05150.03170.0559-0.1762-0.00440.1240.00210.02850.1295-0.00110.016210.6934.058142.513
30.79880.39190.21531.02060.53621.50870.01720.0080.09710.0846-0.08380.13840.1551-0.18180.06660.1126-0.0120.03910.0547-0.00670.030876.863-9.70192.726
41.29660.43270.89620.25050.2820.98850.06470.1646-0.12060.03190.0387-0.05890.08410.2164-0.10330.12360.0080.0170.1028-0.01320.0237104.185-8.8993.932
51.2204-0.2079-0.31030.53480.06461.7189-0.0676-0.1057-0.02720.01740.0348-0.00440.10460.32140.03280.0942-0.00690.04760.1263-0.0010.025667.122-0.139127.349
61.0860.11220.47470.1690.14691.03630.006-0.0797-0.03290.0198-0.01250.03410.0476-0.09430.00650.1199-0.01350.03980.0779-0.01120.046339.6090.264126.488
71.32570.08050.02990.6415-0.12841.8309-0.0130.04420.03160.0172-0.00550.0299-0.0806-0.30950.01850.09570.02460.0370.13130.00910.018447.70837.615108.619
81.2986-0.02490.42940.20960.00430.79360.01360.09370.02210.0125-0.0308-0.0433-0.00330.07650.01710.1162-0.01750.02330.07590.02550.022474.82238.57109.78
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 326
2X-RAY DIFFRACTION2A327 - 558
3X-RAY DIFFRACTION3B94 - 323
4X-RAY DIFFRACTION4B324 - 558
5X-RAY DIFFRACTION5C91 - 322
6X-RAY DIFFRACTION6C323 - 558
7X-RAY DIFFRACTION7D93 - 322
8X-RAY DIFFRACTION8D323 - 558

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