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- PDB-9omj: WrtF fucosyltransferase - GDP-beta-L-fucose -

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Basic information

Entry
Database: PDB / ID: 9omj
TitleWrtF fucosyltransferase - GDP-beta-L-fucose
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / donor / metal-independent / GT-A / O-antigen
Function / homologyGlycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE / Glycosyltransferase
Function and homology information
Biological speciesRhizobium tropici CIAT 899 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)62,2746
Polymers60,9112
Non-polymers1,3634
Water6,377354
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1373
Polymers30,4551
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1373
Polymers30,4551
Non-polymers6812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.910, 65.640, 124.120
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: 30455.408 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-GFB / GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE


Mass: 589.342 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H25N5O15P2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
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: 1.48→46.15 Å / Num. obs: 87116 / % possible obs: 97.8 % / Redundancy: 9.2 % / CC1/2: 0.999 / Net I/σ(I): 13
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 6960 / CC1/2: 0.631 / CC star: 0.88 / % possible all: 99.86

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→46.15 Å / SU ML: 0.1991 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.6521
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 3529 5 %
Rwork0.1743 67087 -
obs0.176 70616 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4025 0 88 354 4467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01474199
X-RAY DIFFRACTIONf_angle_d1.43395704
X-RAY DIFFRACTIONf_chiral_restr0.0759655
X-RAY DIFFRACTIONf_plane_restr0.013724
X-RAY DIFFRACTIONf_dihedral_angle_d14.68221501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.40061390.3762650X-RAY DIFFRACTION99.79
1.62-1.650.30991410.33922668X-RAY DIFFRACTION99.93
1.65-1.670.331380.32522623X-RAY DIFFRACTION99.78
1.67-1.70.35631380.31042632X-RAY DIFFRACTION99.89
1.7-1.720.32711410.30992676X-RAY DIFFRACTION99.82
1.72-1.750.37161400.28052653X-RAY DIFFRACTION99.93
1.75-1.790.29241370.282621X-RAY DIFFRACTION99.86
1.79-1.820.32791420.25922704X-RAY DIFFRACTION99.93
1.82-1.860.2651380.21492627X-RAY DIFFRACTION99.93
1.86-1.90.25851390.2012649X-RAY DIFFRACTION99.96
1.9-1.940.21931410.18492672X-RAY DIFFRACTION99.79
1.94-1.990.21341400.1662668X-RAY DIFFRACTION99.96
1.99-2.040.2111400.16142664X-RAY DIFFRACTION99.93
2.04-2.10.19391410.15722672X-RAY DIFFRACTION99.75
2.1-2.170.18921390.15282655X-RAY DIFFRACTION99.86
2.17-2.250.18971420.15892691X-RAY DIFFRACTION99.75
2.25-2.340.20671410.16292685X-RAY DIFFRACTION99.89
2.34-2.450.19261400.14622659X-RAY DIFFRACTION99.93
2.45-2.570.1741410.14852689X-RAY DIFFRACTION99.82
2.57-2.740.21321430.15292711X-RAY DIFFRACTION99.96
2.74-2.950.19251420.16322705X-RAY DIFFRACTION99.93
2.95-3.240.1831430.15162708X-RAY DIFFRACTION100
3.24-3.710.16891440.15152733X-RAY DIFFRACTION99.83
3.71-4.680.16351460.13962784X-RAY DIFFRACTION99.93
4.68-46.150.24411530.19192888X-RAY DIFFRACTION99.77
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)
12.575380008440.0340954204779-0.6770061854211.37546566136-0.09226325782983.00208229897-0.03235252745790.303814488690.136456649419-0.2791721613560.1403472178610.211038024819-0.135149419984-0.642227648286-0.07385505775970.248529362973-0.00185224695091-0.04574867745730.3847152520530.05922245084710.2368548471573.24574233167-11.3757281678-49.9553554503
22.514777062360.3051038072560.619743102311.50607771534-0.4710702490433.1891355409-0.1360697961450.2149932226690.024873018128-0.197620699890.0353591538024-0.118034305672-0.09897723796110.108069183390.0895779248090.177148339169-0.008806335305990.01772660956070.2214447609670.01515838603570.15044926664221.7805120834-13.4308008839-48.5614985559
35.572219920960.783262238199-0.6110502056125.660568255890.854317402873.81374350296-0.06401389754060.3037059109540.2551752018650.0141485232585-0.0669228273672-0.436745139054-0.2953545575840.8119686983320.1277674672410.206841985481-0.0746570025628-0.04638071856760.4723064461270.05837120080650.26101059160340.1995530387-10.4388391629-39.143842224
43.159507276420.610048841184-0.6027970877011.8231661699-0.530058441513.18171283620.0942519987415-0.330860383818-0.09440068720970.241500633902-0.131135357666-0.167395841796-0.06210353902730.5968002420050.03953090781410.196987676509-0.0063454936158-0.02093041661550.3539322330610.0178729622450.19102838169927.8524112165-13.8242123257-12.7262862735
52.16942680852-0.4519464541860.5128311580480.61689851772-0.2289454826471.362009472040.032472837813-0.03155630986030.002205305507090.062574476081-0.04783199417440.108407512713-0.03254550448020.01025377915980.01253004925730.174209485056-0.02150161843180.01913638603550.202692510831-0.02844975030780.188892453112.48448576086-9.96496034992-15.6235460889
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 4 through 97 )BD4 - 971 - 94
22chain 'B' and (resid 98 through 215 )BD98 - 21595 - 204
33chain 'B' and (resid 216 through 265 )BD216 - 265205 - 254
44chain 'A' and (resid 3 through 79 )AA3 - 791 - 77
55chain 'A' and (resid 80 through 277 )AA80 - 27778 - 268

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