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- PDB-9omn: WrtF fucosyltransferase - GDP-2-deoxy-2-fluoro-beta-L-fucose -

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Basic information

Entry
Database: PDB / ID: 9omn
TitleWrtF fucosyltransferase - GDP-2-deoxy-2-fluoro-beta-L-fucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / inhibitor / metal-independent / GT-A / O-antigen
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / : / GLYCINE / PHOSPHATE ION / Glycosyltransferase
Function and homology information
Biological speciesRhizobium tropici CIAT 899 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)63,32616
Polymers61,0272
Non-polymers2,30014
Water1,08160
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7479
Polymers30,5131
Non-polymers1,2338
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5807
Polymers30,5131
Non-polymers1,0666
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.530, 124.330, 45.770
Angle α, β, γ (deg.)90.000, 93.950, 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-terminally truncated / 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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Non-polymers , 5 types, 74 molecules

#2: Chemical ChemComp-A1CCU / GDP-2-deoxy-2-fluoro-beta-L-fucose


Mass: 591.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24FN5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.02 Å3/Da / Density % sol: 39.25 %
Crystal growTemperature: 277 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: 08B1-1 / Wavelength: 1.181 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 2.07→45.66 Å / Num. obs: 29467 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 9.1
Reflection shellResolution: 2.3→2.382 Å / Mean I/σ(I) obs: 1.92 / Num. unique obs: 2115 / CC1/2: 0.731

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.66 Å / SU ML: 0.3048 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.2714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.259 2872 6.78 %
Rwork0.2104 39505 -
obs0.2137 21529 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4067 0 136 60 4263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264286
X-RAY DIFFRACTIONf_angle_d0.54395828
X-RAY DIFFRACTIONf_chiral_restr0.0437664
X-RAY DIFFRACTIONf_plane_restr0.0041736
X-RAY DIFFRACTIONf_dihedral_angle_d13.85971521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.39871270.36341820X-RAY DIFFRACTION99.69
2.34-2.380.39791450.33511893X-RAY DIFFRACTION99.71
2.38-2.420.32971320.32921956X-RAY DIFFRACTION99.95
2.42-2.470.32491260.30581805X-RAY DIFFRACTION99.54
2.47-2.520.35031460.31791915X-RAY DIFFRACTION99.61
2.52-2.570.3691420.27261918X-RAY DIFFRACTION99.71
2.57-2.630.31451360.2731800X-RAY DIFFRACTION99.79
2.63-2.70.32341370.26611937X-RAY DIFFRACTION99.62
2.7-2.770.26081290.2411854X-RAY DIFFRACTION99.6
2.77-2.850.3361390.23861891X-RAY DIFFRACTION99.8
2.85-2.950.25351290.22661893X-RAY DIFFRACTION99.7
2.95-3.050.26141450.22371904X-RAY DIFFRACTION99.76
3.05-3.170.33441250.20931855X-RAY DIFFRACTION99.75
3.17-3.320.21031380.19541887X-RAY DIFFRACTION99.75
3.32-3.490.20991420.18061878X-RAY DIFFRACTION99.7
3.49-3.710.2421240.19111877X-RAY DIFFRACTION99.8
3.71-40.20781310.1721926X-RAY DIFFRACTION99.81
4-4.40.19961470.161882X-RAY DIFFRACTION100
4.4-5.030.25941490.17431876X-RAY DIFFRACTION99.9
5.03-6.340.26751440.21231866X-RAY DIFFRACTION99.41
6.34-45.660.2261390.19231872X-RAY DIFFRACTION99.55
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)
13.528219097710.00976012080039-0.664829478694.91797347999-0.896516139223.54400866796-0.0358400973503-0.3138210905110.19521523310.6799795164670.1507429341560.447478576087-0.147970691626-0.153859960133-0.08657891727970.5390991130580.0163979245820.1786269100990.241120379485-0.01891086033430.481500713668-17.692636781-11.090923754-1.09007903787
23.766805518-0.734446847627-1.596320142042.900854210160.8886477950433.10728904430.02276360834660.1876474357990.0562113200896-0.6328619680910.115852066955-0.640706964873-0.1810395120240.398288974678-0.1227719797220.626750829082-0.07454148422120.2222706963820.350429936998-0.04045663706810.5336448096430.503909831737-15.8401318811-16.5414457835
32.514779408160.139758506088-1.023951202284.85106583660.7475617153964.548946217550.04795725076960.0855307515498-0.319801377315-0.6770184281520.195002087904-1.244651328190.03954358411050.469897303901-0.2159340346430.6606572539180.05279022180950.3038411566640.333490322038-0.0134866391230.755638848137-0.174924155211-49.2285967658-18.5411521594
45.10369470546-0.5820054100581.418571054855.745403643991.191126845383.958050535-0.131333059341-0.00993303038476-0.7599803228730.153665517558-0.101246101825-0.07044929915910.777217407663-0.1573777899440.2244869675330.6554963611990.03397626827330.1963074966150.258323212801-0.01593105268870.44892167851-10.4650485339-57.1130238097-10.98462822
53.08069831369-0.0863293882646-0.6833501209434.34289850245-1.815136554463.36976852321-0.01798580565420.109322293262-0.1670583360351.20171414044-0.0570992409190.2797074893920.218302830135-0.117723066744-0.007543075693320.4820253542730.05052996733080.05835071451630.1711963739530.007646520332460.329945165978-14.7382600784-45.9595216083-4.39041891946
65.926718890350.610551855041-0.3320898608490.204621698994-0.8573610544254.769323612440.111036135963-0.7238433645270.05311491383650.0832093450137-0.202477050987-0.3058466630460.0714957534564-0.003387324057360.06890313933870.7387244741020.07162188662870.1337344987950.369231302822-0.07565518592050.538845295701-9.34206061091-52.7222826715-2.70633915515
79.29930969817-0.245851283741-2.010943125241.085591404750.5941336462614.815039719170.0756699195445-0.4693567727170.9005582290560.638213337090.2119042711140.00516092513849-0.1033295865990.102274033826-0.1348996083370.7467484243060.08177701834680.1460935049290.289485697482-0.03339871256580.51230018254-15.7919613836-34.73778505176.85204360935
86.711106635412.624761196661.267067684256.34867005292-2.909083722322.614328386570.298393806186-1.47771798273-0.9824950862521.52068110167-0.446563552638-0.355342178727-0.1892970501490.5109603055110.3907900774571.343027034740.0604652305490.6436637277820.663707065345-0.1508378550420.885164622306-24.9023220545-37.014351564815.4473782368
91.53827319161.84970863289-1.993763553932.33295527174-1.732209582324.56539535765-0.4153464770320.2730567937810.02042445696420.8091648963720.02636798373331.181957534450.784933392325-0.6178737963980.2926610750051.157823091670.0570606569540.5606434775490.5630390322540.02678885077140.952019730614-32.8300453368-42.945930750211.163505502
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 97 )AA3 - 971 - 95
22chain 'A' and (resid 98 through 302 )AA - C98 - 30296 - 257
33chain 'B' and (resid 3 through 78 )BE3 - 781 - 76
44chain 'B' and (resid 79 through 119 )BE79 - 11977 - 117
55chain 'B' and (resid 120 through 176 )BE120 - 176118 - 174
66chain 'B' and (resid 177 through 200 )BE177 - 200175 - 195
77chain 'B' and (resid 201 through 231 )BE201 - 231196 - 226
88chain 'B' and (resid 232 through 250 )BE232 - 250227 - 244
99chain 'B' and (resid 251 through 278 )BE251 - 278245 - 272

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