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- PDB-9omk: WrtF fucosyltransferase - trisaccharide acceptor -

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Basic information

Entry
Database: PDB / ID: 9omk
TitleWrtF fucosyltransferase - trisaccharide acceptor
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / acceptor / metal-independent / GT-A / O-antigen
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / GUANOSINE-5'-MONOPHOSPHATE / : / beta-D-glucopyranose / alpha-L-fucopyranose / Glycosyltransferase
Function and homology information
Biological speciesRhizobium tropici CIAT 899 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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)63,08314
Polymers61,0272
Non-polymers2,05612
Water1,58588
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5417
Polymers30,5131
Non-polymers1,0286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5417
Polymers30,5131
Non-polymers1,0286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.450, 65.620, 128.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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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

#4: 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
#5: Sugar ChemComp-A1CCV / 6-deoxy-alpha-D-talopyranose


Type: D-saccharide / Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
#6: 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

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Non-polymers , 3 types, 94 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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 293 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: Sep 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.86→45.98 Å / Num. obs: 46457 / % possible obs: 99.9 % / Redundancy: 13.4 % / Biso Wilson estimate: 36.51 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.9
Reflection shellResolution: 2.05→2.123 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3392 / CC1/2: 0.711

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.84 Å / SU ML: 0.2748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.1794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.242 1739 5 %
Rwork0.2107 33025 -
obs0.2123 34764 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.73 Å2
Refinement stepCycle: LAST / Resolution: 2.05→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4044 0 128 88 4260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284255
X-RAY DIFFRACTIONf_angle_d0.64865783
X-RAY DIFFRACTIONf_chiral_restr0.0463678
X-RAY DIFFRACTIONf_plane_restr0.0042728
X-RAY DIFFRACTIONf_dihedral_angle_d14.16611517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.110.35881420.37322677X-RAY DIFFRACTION99.72
2.11-2.180.40191430.34912715X-RAY DIFFRACTION99.69
2.18-2.260.35811420.3142709X-RAY DIFFRACTION99.89
2.26-2.350.32921430.29462716X-RAY DIFFRACTION99.97
2.35-2.450.31041420.26112712X-RAY DIFFRACTION99.65
2.45-2.580.31111450.24842744X-RAY DIFFRACTION99.83
2.58-2.740.27091430.2452716X-RAY DIFFRACTION99.79
2.74-2.960.2691450.23672760X-RAY DIFFRACTION99.79
2.96-3.250.26241440.21422747X-RAY DIFFRACTION99.9
3.25-3.720.22951470.20442772X-RAY DIFFRACTION99.79
3.72-4.690.21231480.17112820X-RAY DIFFRACTION99.9
4.69-45.840.19571550.182937X-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)
17.97383617998-1.402869026271.018035390414.26495471303-0.647094205771.98730257553-0.0145379787772-0.4047309189770.0823986795411-0.147287203303-0.160438930161-0.4793855817090.1221491420190.4692346921680.1811949211440.396616113769-0.1548300434270.06606957592010.549169312801-0.003199794557470.397415266851-0.611532321712-19.807730007113.7860908985
26.519138347031.69758516792-2.274096544811.47294485211-0.9793148796523.90365346224-0.1721461700710.6006274331190.0968599335248-0.3415812268970.07617610400560.07912610824310.00925885158291-0.1712149893980.0957958937930.512971644122-0.139693958222-0.04013552967180.523971708968-0.02510252369960.309219954213-17.5379784002-20.11225238759.28046997874
35.016279247240.16238641131-1.059599048871.40494418116-0.118152408052.40699908908-0.0721880465801-0.0954492244024-0.326352811615-0.05433206555630.1292513926640.2314357264470.151013620167-0.197860684749-0.06086147270950.419288386378-0.149041559198-0.02224342177440.533221919962-0.01848241076840.412740631238-30.6824948377-26.241105454421.2269500134
46.290034771351.69090903375-0.7216403912283.65141362912-0.5461656772466.31313745661-0.272476959054-0.550628102615-0.220185541389-0.01238731515580.1390291940770.594572714459-0.193941860939-1.853703158210.1560905419670.4200741021970.00831037939214-0.001528370448021.104783475430.0339059594070.542431730399-26.5748255929-23.109112106950.155956493
56.933696891250.1062549168033.411734017389.09616224149-3.033276807976.85675795381-0.204021527344-1.39975088715-0.2799571641870.0472774916420.090021303872-0.00374461837055-0.699118045078-1.063397712740.06873618356150.443856625429-0.0304428771207-0.05937889141110.645245451376-0.02046363763670.426578747836-18.7583913304-21.760788383956.1509616405
61.86080078777-0.0414283253541.648698876860.533752890170.5590575769316.23123894253-0.2999017895050.1236972423150.240330434837-0.1080087004070.2214883933-0.185472058002-0.7350874580640.8376914079870.07754019668550.45809846094-0.1912578801820.01021363249950.6476703598360.004162228712450.411723245628-7.61227529139-19.228556898650.9331710292
73.49998087267-1.95655480999-1.693201463961.055611654280.1486230687739.0751960968-0.2652280330650.0630312938411-0.09892177037-0.1181846252220.06937034033430.284058993311-0.5291273329641.236624973710.2274512736640.400967564556-0.218525667484-0.0174582273360.7855153440270.0752037249330.510391864559-5.05385322962-24.899125772647.4075230515
85.22874856480.081127187512-4.605535802759.80162135643-6.00424220048.239792403870.47676514492-0.762159566578-1.99237057258-0.2530290724790.1287323716581.13850334590.3397785898060.133643982462-0.1721325083530.426349647595-0.196486390788-0.1014478983571.025656669160.2588053940860.8790749404687.67599331606-26.295172530137.257809937
92.339291866531.55485931408-0.9643368043838.38684894986-2.241031158154.277411590680.301232187169-1.99458192056-0.812904917851-0.392463543939-0.462705608135-0.8624668571010.5645471467771.01232804930.2416528806410.536463790211-0.298563620994-0.03932639638591.463511251080.1235303704820.88255679692113.7322884701-22.414520373842.2553666697
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 155 )AA80 - 15578 - 153
33chain 'A' and (resid 156 through 277 )AA156 - 277154 - 269
44chain 'B' and (resid 4 through 79 )BF4 - 791 - 76
55chain 'B' and (resid 80 through 97 )BF80 - 9777 - 94
66chain 'B' and (resid 98 through 176 )BF98 - 17695 - 173
77chain 'B' and (resid 177 through 215 )BF177 - 215174 - 206
88chain 'B' and (resid 216 through 231 )BF216 - 231207 - 222
99chain 'B' and (resid 232 through 264 )BF232 - 264223 - 255

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