PDB-9omm: WrtF fucosyltransferase - tetrasaccharide product

ID or keywords:

Entry

Database: PDB / ID: 9omm

Title

WrtF fucosyltransferase - tetrasaccharide product

Components

Glycosyltransferase

Keywords

TRANSFERASE / product / metal-independent / GT-A / O-antigen

Function / homology

Glycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / GUANOSINE-5'-MONOPHOSPHATE / : / alpha-L-fucopyranose / GUANOSINE / Glycosyltransferase

Function and homology information

Biological species

Rhizobium tropici CIAT 899 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Forrester, T.J.B. / Kimber, M.S.

Funding support

Canada, 1items

Citation

Journal: 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

Deposition	May 14, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 29, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9omm.cif.gz	375.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9omm.ent.gz		Display	PDB format
PDBx/mmJSON format	9omm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9omm_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	9omm_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9omm_validation.xml.gz	24.2 KB	Display
Data in CIF	9omm_validation.cif.gz	30.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/9omm ftp://data.pdbj.org/pub/pdb/validation_reports/om/9omm	HTTPS FTP

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Related structure data

Related structure data	9omhC 9omiC 9omjC 9omkC 9omlC 9omnC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (3) #104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #75 - Mar 2006 Tissue Factor similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Glycosyltransferase

B: Glycosyltransferase

hetero molecules

62.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycosyltransferase

hetero molecules

defined by author
30.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glycosyltransferase

hetero molecules

defined by author
31.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.640, 65.670, 128.400
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P22₁2₁
Space group name Hall	P22ab(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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Protein , 1 types, 2 molecules AB

#1: Protein	Glycosyltransferase Mass: 30499.416 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

#1: Protein

Glycosyltransferase

Mass: 30499.416 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, 3 molecules

#2: Polysaccharide

alpha-L-fucopyranose-(1-4)-beta-D-glucopyranose

Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1 / Source method: obtained synthetically

Descriptor	Type	Program
LFucpa1-4DGlcpb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a1221m-1a_1-5]/1-2/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-L-Fucp]{}}	LINUCS	PDB-CARE

#6: 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.: 1 / Source method: obtained synthetically / Formula: C₆H₁₂O₅ / Feature type: SUBJECT OF INVESTIGATION

#7: Sugar

ChemComp-A1CCW / 2-O-acetyl-6-deoxy-alpha-D-talopyranose

Type: D-saccharide, alpha linking / Mass: 206.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₄O₆ / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 4 types, 17 molecules

#3: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-GMP / GUANOSINE Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₅ / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.23 Å³/Da / Density % sol: 44.94 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.181 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.181 Å / Relative weight: 1
Reflection	Resolution: 2.25→46.07 Å / Num. obs: 26660 / % possible obs: 100 % / Redundancy: 13 % / B_iso Wilson estimate: 57.45 Å² / CC_1/2: 1 / R_rim(I) all: 0.067 / Net I/σ(I): 24.91
Reflection shell	Resolution: 2.25→2.3 Å / Redundancy: 13.4 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 1663 / CC_1/2: 0.593 / R_rim(I) all: 2.88 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.25→46.07 Å / SU ML: 0.4181 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.6971
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2653	4224	8.45 %
R_work	0.2155	45776	-
obs	0.2197	26646	99.79 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 70.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→46.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4083	0	93	14	4190

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0021	4255
X-RAY DIFFRACTION	f_angle_d	0.5053	5779
X-RAY DIFFRACTION	f_chiral_restr	0.0433	672
X-RAY DIFFRACTION	f_plane_restr	0.0032	735
X-RAY DIFFRACTION	f_dihedral_angle_d	13.2607	1520

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.25-2.28	0.6435	135	0.5859	1499	X-RAY DIFFRACTION	99.27
2.28-2.3	0.5149	145	0.4731	1561	X-RAY DIFFRACTION	99.82
2.3-2.33	0.4211	133	0.4008	1516	X-RAY DIFFRACTION	99.82
2.33-2.36	0.3571	155	0.3516	1534	X-RAY DIFFRACTION	99.94
2.36-2.39	0.4095	132	0.3288	1505	X-RAY DIFFRACTION	99.27
2.39-2.42	0.3217	130	0.3118	1536	X-RAY DIFFRACTION	99.23
2.42-2.46	0.3381	146	0.3283	1468	X-RAY DIFFRACTION	99.45
2.46-2.5	0.361	142	0.3272	1584	X-RAY DIFFRACTION	99.77
2.5-2.53	0.3893	144	0.3493	1473	X-RAY DIFFRACTION	99.69
2.53-2.58	0.3859	139	0.3355	1548	X-RAY DIFFRACTION	99.7
2.58-2.62	0.2968	152	0.3016	1547	X-RAY DIFFRACTION	99.88
2.62-2.67	0.3754	126	0.2708	1506	X-RAY DIFFRACTION	99.94
2.67-2.72	0.3121	138	0.2649	1528	X-RAY DIFFRACTION	99.64
2.72-2.77	0.3386	140	0.2369	1535	X-RAY DIFFRACTION	99.7
2.77-2.83	0.3248	131	0.2395	1522	X-RAY DIFFRACTION	99.7
2.83-2.9	0.295	147	0.2412	1519	X-RAY DIFFRACTION	99.88
2.9-2.97	0.3182	145	0.2501	1552	X-RAY DIFFRACTION	100
2.97-3.05	0.2756	135	0.2385	1527	X-RAY DIFFRACTION	99.88
3.05-3.14	0.3382	139	0.2428	1529	X-RAY DIFFRACTION	99.94
3.14-3.24	0.284	142	0.2202	1518	X-RAY DIFFRACTION	100
3.24-3.36	0.2736	152	0.2193	1523	X-RAY DIFFRACTION	100
3.36-3.5	0.2227	143	0.2059	1500	X-RAY DIFFRACTION	99.94
3.5-3.65	0.2395	150	0.211	1554	X-RAY DIFFRACTION	100
3.65-3.85	0.2906	122	0.1861	1547	X-RAY DIFFRACTION	99.94
3.85-4.09	0.2366	154	0.1804	1494	X-RAY DIFFRACTION	100
4.09-4.4	0.2153	144	0.157	1553	X-RAY DIFFRACTION	100
4.4-4.85	0.2117	138	0.1701	1524	X-RAY DIFFRACTION	100
4.85-5.55	0.2047	148	0.1771	1520	X-RAY DIFFRACTION	99.94
5.55-6.98	0.2414	139	0.207	1522	X-RAY DIFFRACTION	99.94
6.98-46.07	0.2172	138	0.1721	1532	X-RAY DIFFRACTION	99.52

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	5.73111020989	0.0946043720349	-2.09882057397	1.52829689033	-0.883270720502	4.83537164306	-0.39607598556	0.321353721319	-0.267259255849	-0.12693206119	0.272062828528	0.225785310854	0.641432963827	-0.428511008935	0.129844343325	0.492554998651	-0.0436892385656	0.00441336647796	0.379568719454	-0.00548230657543	0.397703775018	13.4942400494	22.0276982493	11.5206031845
2	3.86677164584	1.21123968483	0.302968370453	0.672759899102	0.217249128532	7.49872014892	-0.137243507429	-0.0737403007197	-0.132082721845	0.0867561030185	-0.0324871313505	-0.0395319010163	0.696896268693	0.48645189292	0.189995575199	0.505811324052	0.142002551279	0.0784292720087	0.419685608933	0.0428187729575	0.457666534036	24.9692577714	21.7774345895	18.3132375359
3	4.19932384839	3.46590413575	-1.21253710321	4.46610940773	2.18357638579	8.99172364959	0.359170380026	1.238549626	0.839555104463	0.306365538018	-0.118137242101	-0.730906616588	-0.72505414432	0.497157884805	-0.111421886628	0.504174757705	0.154832438756	-0.0337697622503	0.862704798471	0.240773047471	0.785186794521	44.3279242648	25.1682621359	24.3426376195
4	4.93974760553	1.70156684384	-2.42630439889	3.73526834219	-1.95796412849	5.26571925228	0.0933197176205	-0.0430017184432	0.0151153021463	0.413071969693	-0.226699591969	-0.479013690174	-0.0764961267461	0.463103457534	0.191561101612	0.549039859539	0.114910505787	-0.0705213259259	0.425554324075	0.0538684777917	0.461716685264	32.115141803	20.0493355601	50.4926617546
5	4.24086042656	-0.384393066669	1.27052740508	1.63761468985	-0.726569352812	1.34460831985	-0.00177990380963	-0.246249132521	0.200074603418	0.344756619889	0.00712379141691	0.192334548256	-0.114002909335	-0.247336573468	0.0031245826905	0.548991307614	0.117595901363	0.0835849402583	0.388274917965	-0.0608283672915	0.42196497699	7.10521094522	24.2620545309	47.5273585022

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 141 )	A	A	3 - 141	1 - 139
2	2	chain 'A' and (resid 142 through 215 )	A	A	142 - 215	140 - 209
3	3	chain 'A' and (resid 216 through 264 )	A	A	216 - 264	210 - 258
4	4	chain 'B' and (resid 3 through 79 )	B	D	3 - 79	1 - 77
5	5	chain 'B' and (resid 80 through 277 )	B	D	80 - 277	78 - 271

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