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- PDB-9omi: WrtF fucosyltransferase - GDP -

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Basic information

Entry
Database: PDB / ID: 9omi
TitleWrtF fucosyltransferase - GDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / fucose / metal-independent / GT-A / O-antigen
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / GUANOSINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesRhizobium tropici CIAT 899 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: WrtF from Rhizobium tropici CIAT 899 is a GT-A fold fucosyltransferase that binds its donor nonproductively.
Authors: Forrester, T.J.B. / Lin, S. / Lowary, T.L. / Kimber, M.S.
History
DepositionMay 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2025Group: 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 / _citation_author.identifier_ORCID / _citation_author.name

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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)62,1947
Polymers61,0272
Non-polymers1,1675
Water5,332296
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0493
Polymers30,5131
Non-polymers5352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1454
Polymers30,5131
Non-polymers6313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.830, 65.960, 123.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#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
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.13 %
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: Sep 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
ReflectionResolution: 1.97→46.24 Å / Num. obs: 37512 / % possible obs: 98.3 % / Redundancy: 8.9 % / CC1/2: 0.999 / Net I/σ(I): 14.1
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.41 / Num. unique obs: 3219 / CC1/2: 0.592 / CC star: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→46.24 Å / SU ML: 0.2193 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3505
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2342 1873 5 %
Rwork0.187 35604 -
obs0.1898 37477 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.16 Å2
Refinement stepCycle: LAST / Resolution: 1.97→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 73 296 4401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484187
X-RAY DIFFRACTIONf_angle_d0.76765686
X-RAY DIFFRACTIONf_chiral_restr0.0499648
X-RAY DIFFRACTIONf_plane_restr0.0052724
X-RAY DIFFRACTIONf_dihedral_angle_d16.97791523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.3091220.30162309X-RAY DIFFRACTION84.35
2.02-2.080.30191350.26352568X-RAY DIFFRACTION93.5
2.08-2.150.28921440.2312729X-RAY DIFFRACTION99.38
2.15-2.230.28841440.22112735X-RAY DIFFRACTION99.76
2.23-2.320.28071440.22692761X-RAY DIFFRACTION99.69
2.32-2.420.22651460.19172756X-RAY DIFFRACTION99.9
2.42-2.550.2581440.17292758X-RAY DIFFRACTION99.76
2.55-2.710.23291460.17062780X-RAY DIFFRACTION99.97
2.71-2.920.22071470.19072780X-RAY DIFFRACTION99.93
2.92-3.210.2341450.17422786X-RAY DIFFRACTION99.86
3.21-3.680.21281500.17012832X-RAY DIFFRACTION100
3.68-4.630.18611490.14772838X-RAY DIFFRACTION99.9
4.63-46.240.25091570.20542972X-RAY DIFFRACTION99.81
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)
12.45279304888-0.0414949544781-0.485709961160.74718355981-0.1615972783250.9522972312320.00300683875311-0.195273444333-0.09763361273350.166296417677-0.0511070119957-0.137557204522-0.006738840238340.319530359550.04346847475540.298876000054-0.0299450552237-0.0156533876840.3517735134680.01243369034320.25006710165920.2647377794-12.7445992491-10.0293225327
24.15283259179-0.463430695471.205054669111.64619604979-0.3407864794343.553840928730.05258350655840.1960518639190.0495310783982-0.0111668962104-0.1328667180540.02358539178520.005615069365570.0536768545680.1292303777360.1802474610980.009558865360550.01947858759820.253236962268-0.0471229617080.2120387222448.54168986461-12.4113020351-17.1110511539
32.77262878177-1.22114583633-1.566730663393.402290949190.5632745837525.220816820330.06371967936380.0730159921635-0.0304536078967-0.00442849301442-0.0859337076910.284198022651-0.125334359235-0.1302475011550.0751631277080.1771816453810.00670020800292-0.03371592079730.285579808387-0.01489976138560.299894886028-11.5148312266-6.32447415363-21.893246622
42.92054202281-0.603767766195-0.974035769312.496445186850.2763492740083.80807079745-0.08658038759080.2186392031410.12073372717-0.2294879282380.1418609586370.305517168655-0.131553748058-0.6000730236580.009702412694530.243734611269-0.012443478705-0.03466307833830.4158357049080.04022446834580.2981203471771.7247307283-11.4132311955-48.8010184983
52.85013207133-0.0982487729050.3136524233091.76589013198-0.5326125468842.2556496904-0.1210704452740.215186647130.00607037384563-0.1911292460570.0799087317433-0.111089870069-0.115515019480.09424904217310.06261846776760.268170613984-0.01038313928180.01588658220220.3520600657590.01792379964740.23059527665120.0708777671-13.1994075552-49.2387641798
64.220392412130.357312021653-0.9759027183587.066347307880.8838945484576.23397861186-0.03579491649550.3849094384880.3960639301330.0230901562487-0.0585528997737-0.510292561446-0.471378003410.8360034963060.1125757163030.283489136514-0.063517414108-0.05271522651890.5540670837340.04669815605420.36407444214140.0247830837-10.2953457716-38.9802723402
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 141 )AA3 - 1411 - 139
22chain 'A' and (resid 142 through 215 )AA142 - 215140 - 205
33chain 'A' and (resid 216 through 277 )AA216 - 277206 - 267
44chain 'B' and (resid 4 through 79 )BD4 - 791 - 76
55chain 'B' and (resid 80 through 215 )BD80 - 21577 - 205
66chain 'B' and (resid 216 through 265 )BD216 - 265206 - 255

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