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- PDB-9oml: WrtF fucosyltransferase - acetylated trisaccharide acceptor -

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Basic information

Entry
Database: PDB / ID: 9oml
TitleWrtF fucosyltransferase - acetylated trisaccharide acceptor
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / acetylated acceptor / metal-independent / GT-A / O-antigen
Function / homology
Function and homology information


hexosyltransferase activity
Similarity search - Function
Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / : / beta-D-glucopyranose / alpha-L-fucopyranose / OCTAN-1-OL / Glycosyltransferase
Similarity search - Component
Biological speciesRhizobium tropici CIAT 899 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsForrester, T.J.B. / Kimber, M.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2020-07113 Canada
CitationJournal: To Be Published
Title: WrtF from Rhizobium tropici CIAT 899 is a GT-A fold fucosyltransferase which binds its donor non-productively
Authors: Forrester, T.J.B. / Kimber, M.S. / Lowary, T.L. / Lin, S.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,61218
Polymers61,0272
Non-polymers2,58516
Water4,234235
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,89810
Polymers30,5131
Non-polymers1,3849
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7148
Polymers30,5131
Non-polymers1,2007
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.150, 122.350, 45.590
Angle α, β, γ (deg.)90.000, 93.516, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycosyltransferase


Mass: 30513.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal truncation / Source: (gene. exp.) Rhizobium tropici CIAT 899 (bacteria) / Cell: bacterial / Gene: GXW80_17485 / Plasmid: pET28a / Cell (production host): bacterial / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P1C6J0

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Sugars , 3 types, 6 molecules

#5: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar ChemComp-A1CCW / 2-O-acetyl-6-deoxy-alpha-D-talopyranose


Type: D-saccharide, alpha linking / Mass: 206.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H14O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 245 molecules

#2: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical ChemComp-OC9 / OCTAN-1-OL


Mass: 130.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 200 mM ammonium sulfate, 100 mM HEPES pH 7.5, 35% poly (acrylic acid sodium salt) 2100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.61→45.5 Å / Num. obs: 60682 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.994 / Net I/σ(I): 4.9
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 3674 / CC1/2: 0.442

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.07 Å / SU ML: 0.273 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.6564
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2332 2410 3.29 %
Rwork0.1941 70775 -
obs0.1954 37063 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.78 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 162 235 4511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00594353
X-RAY DIFFRACTIONf_angle_d0.84155907
X-RAY DIFFRACTIONf_chiral_restr0.0495689
X-RAY DIFFRACTIONf_plane_restr0.0069742
X-RAY DIFFRACTIONf_dihedral_angle_d18.49811559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.38041520.36194085X-RAY DIFFRACTION99.46
1.94-1.980.33541520.31714187X-RAY DIFFRACTION99.77
1.98-2.030.33761300.30294152X-RAY DIFFRACTION99.91
2.03-2.080.34291340.28384197X-RAY DIFFRACTION99.84
2.08-2.130.3151520.26714119X-RAY DIFFRACTION99.84
2.13-2.20.23911520.23994145X-RAY DIFFRACTION99.86
2.2-2.270.27211380.22444228X-RAY DIFFRACTION99.91
2.27-2.350.30311330.224143X-RAY DIFFRACTION99.86
2.35-2.440.24251420.19964155X-RAY DIFFRACTION99.88
2.44-2.550.25091410.19014180X-RAY DIFFRACTION99.88
2.55-2.690.23621290.19074200X-RAY DIFFRACTION100
2.69-2.860.19771370.17754201X-RAY DIFFRACTION100
2.86-3.080.23531310.16684196X-RAY DIFFRACTION99.91
3.08-3.390.19471600.16984106X-RAY DIFFRACTION99.93
3.39-3.880.20561520.15084143X-RAY DIFFRACTION99.81
3.88-4.880.15571380.14934168X-RAY DIFFRACTION99.7
4.88-43.070.23991370.1954170X-RAY DIFFRACTION99.61
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)
11.56218842757-0.0146633708735-0.9570770631986.78862552671.098572605413.829306907140.07863901818230.2014672269190.253006436233-0.4600688699850.0516719877384-0.376912667013-0.2126354456140.196011268349-0.1303484941240.163990583891-0.004946479579560.00931557822120.1988824809640.02503780340650.2397997149118.3934192194-16.047515151-0.0146578563086
22.489593255520.968473020451-1.330462829313.32391678598-1.243916795212.065204234950.0618922467034-0.02584763887660.09482605765270.2406784766480.06278726565550.294048174538-0.135549821457-0.162074915332-0.1258861841480.231478059450.0415765173204-0.007187859689380.1659794886250.001937162748170.1862047836940.362026706454-18.78271086916.0817146878
33.4213989663-0.378821392749-1.400590914466.24663310193-0.3661474370662.3181999489-0.0684990816311-0.0964793166548-0.2926500896620.3985460582250.02162621234620.716184408470.190261712021-0.2055630804520.04064198017540.257812051487-0.01887281249150.04535182216220.210266830843-0.005614973114010.2272431717110.565378520598-52.368307652218.2873389818
41.869939912120.638380051403-0.9710528097352.69168040725-1.104405172462.64645713238-0.102693369930.150943654301-0.0717735555899-0.3828999355480.0412521027478-0.1743722645750.1910232540480.04442647589650.03454410285330.269152223234-0.02442132890390.01521320800160.160926093624-0.04469945461870.18934282167616.4778796031-49.0131210815-1.07385779612
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 79 )AA3 - 791 - 77
22chain 'A' and (resid 80 through 266 )AA80 - 26678 - 257
33chain 'B' and (resid 3 through 79 )BG3 - 791 - 77
44chain 'B' and (resid 80 through 278 )BG80 - 27878 - 276

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