PDB-9omh: WrtF fucosyltransferase - Apo

ID or keywords:

Entry

Database: PDB / ID: 9omh

Title

WrtF fucosyltransferase - Apo

Components

Glycosyltransferase

Keywords

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

Function / homology

Glycosyltransferase 2-like / Glycosyl transferase family 2 / hexosyltransferase activity / Nucleotide-diphospho-sugar transferases / IMIDAZOLE / Glycosyltransferase

Function and homology information

Biological species

Rhizobium tropici CIAT 899 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.45 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	9omh.cif.gz	743.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9omh.ent.gz	513.7 KB	Display	PDB format
PDBx/mmJSON format	9omh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9omh_validation.pdf.gz	464.3 KB	Display	wwPDB validaton report
Full document	9omh_full_validation.pdf.gz	469.1 KB	Display
Data in XML	9omh_validation.xml.gz	57 KB	Display
Data in CIF	9omh_validation.cif.gz	77.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/9omh ftp://data.pdbj.org/pub/pdb/validation_reports/om/9omh	HTTPS FTP

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Related structure data

Related structure data	9omiC 9omjC 9omkC 9omlC 9ommC 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) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: Glycosyltransferase

B: Glycosyltransferase

C: Glycosyltransferase

D: Glycosyltransferase

hetero molecules

122 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glycosyltransferase

hetero molecules

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

2

B: Glycosyltransferase

hetero molecules

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

3

C: Glycosyltransferase

hetero molecules

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

4

D: Glycosyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.180, 124.290, 64.770
Angle α, β, γ (deg.)	90.000, 93.005, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	Glycosyltransferase Mass: 30513.439 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: truncated C-terminus / Source: (gene. exp.) Rhizobium tropici CIAT 899 (bacteria) / Cell: bacterial / Gene: GXW80_17485 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P1C6J0
#2: Chemical	ChemComp-IMD / IMIDAZOLE Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₅N₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1008 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.11 Å³/Da / Density % sol: 41.81 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 23, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 1.35→46.77 Å / Num. obs: 216717 / % possible obs: 97.9 % / Redundancy: 6.5 % / CC_1/2: 0.998 / Net I/σ(I): 8.5
Reflection shell	Resolution: 1.45→1.502 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 17844 / CC_1/2: 0.435 / CC star: 0.779 / % possible all: 99.88

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1-4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.45→46.77 Å / SU ML: 0.1978 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1908	8934	5 %
R_work	0.1647	169728	-
obs	-	178662	99.92 %

Solvent computation

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

Displacement parameters

B_iso mean: 33.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→46.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8226	0	22	1008	9256

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0041	8394
X-RAY DIFFRACTION	f_angle_d	0.6709	11369
X-RAY DIFFRACTION	f_chiral_restr	0.0622	1300
X-RAY DIFFRACTION	f_plane_restr	0.0064	1479
X-RAY DIFFRACTION	f_dihedral_angle_d	14.6481	3039

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 (%)
1.45-1.47	0.4028	298	0.3772	5648	X-RAY DIFFRACTION	99.77
1.47-1.48	0.3776	297	0.3443	5649	X-RAY DIFFRACTION	99.9
1.48-1.5	0.3202	297	0.3122	5639	X-RAY DIFFRACTION	99.97
1.5-1.52	0.3418	296	0.3052	5620	X-RAY DIFFRACTION	100
1.52-1.54	0.3463	298	0.3122	5670	X-RAY DIFFRACTION	99.97
1.54-1.56	0.331	298	0.2879	5653	X-RAY DIFFRACTION	100
1.56-1.58	0.2605	296	0.2521	5636	X-RAY DIFFRACTION	100
1.58-1.61	0.2566	300	0.2401	5688	X-RAY DIFFRACTION	100
1.61-1.63	0.254	294	0.2178	5596	X-RAY DIFFRACTION	99.98
1.63-1.66	0.247	299	0.2077	5670	X-RAY DIFFRACTION	99.97
1.66-1.69	0.2522	297	0.2026	5646	X-RAY DIFFRACTION	99.98
1.69-1.72	0.2521	296	0.1947	5620	X-RAY DIFFRACTION	99.98
1.72-1.75	0.2144	300	0.1842	5702	X-RAY DIFFRACTION	99.98
1.75-1.79	0.1885	296	0.1822	5619	X-RAY DIFFRACTION	99.98
1.79-1.83	0.2223	296	0.1795	5634	X-RAY DIFFRACTION	100
1.83-1.87	0.2189	299	0.1868	5668	X-RAY DIFFRACTION	99.98
1.87-1.92	0.2424	298	0.1834	5667	X-RAY DIFFRACTION	99.97
1.92-1.97	0.1824	298	0.1642	5659	X-RAY DIFFRACTION	99.92
1.97-2.03	0.1828	298	0.1599	5667	X-RAY DIFFRACTION	99.98
2.03-2.09	0.1875	297	0.1597	5644	X-RAY DIFFRACTION	99.98
2.09-2.17	0.181	298	0.1555	5651	X-RAY DIFFRACTION	99.97
2.17-2.25	0.1781	297	0.1518	5655	X-RAY DIFFRACTION	99.98
2.25-2.36	0.1956	298	0.1545	5663	X-RAY DIFFRACTION	99.95
2.36-2.48	0.1869	299	0.1544	5669	X-RAY DIFFRACTION	99.97
2.48-2.63	0.1971	298	0.1576	5670	X-RAY DIFFRACTION	100
2.63-2.84	0.194	299	0.1651	5674	X-RAY DIFFRACTION	99.92
2.84-3.12	0.189	298	0.1626	5659	X-RAY DIFFRACTION	99.78
3.12-3.58	0.1599	300	0.1486	5692	X-RAY DIFFRACTION	99.87
3.58-4.5	0.1466	298	0.1244	5675	X-RAY DIFFRACTION	99.78
4.5-46.77	0.169	301	0.1525	5725	X-RAY DIFFRACTION	99.26

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	3.41697437432	-2.17868832168	2.15196456795	5.34388714226	-2.81754211481	5.79743712306	-0.00988473140914	-0.210672863833	0.0820430016338	0.415241307902	0.0415472318135	-0.0332225267005	-0.315828629926	0.036769081829	-0.0214549853698	0.231502349837	0.0020124066874	0.0617910682379	0.173036241996	-0.0289605914918	0.128422967001	17.5344132163	-10.1951779721	45.0091349618
2	0.584206873179	-0.124239178258	-0.147371102186	1.99811304451	0.103158883342	1.58076088252	-0.0278139308911	-0.0343242101937	0.0733563563559	0.195018854577	0.0609000980875	0.114539342072	-0.166012180532	-0.0802688155205	-0.0356560933887	0.166545537605	0.0155226008784	0.00607863636184	0.156967391617	0.000603615327838	0.166385887858	16.9990405348	-11.1069138696	31.7883753443
3	0.413856915794	-0.278907951621	-0.172706104548	3.32825556924	0.451370716776	2.53620291837	-0.0351944251112	0.0295995439239	0.0290110372111	0.0103434357319	0.0610562540213	-0.0303236024466	0.0739314157826	0.0697213406137	-0.0214521183035	0.122617531036	-0.0068085693426	0.00388781411869	0.16063595805	0.00828043017749	0.135555705649	18.8816948864	-18.0117800222	25.5531743789
4	2.72031333796	0.453079843335	0.389330242319	2.57523816066	-0.182742858664	4.74864221253	-0.079784305045	0.212690668644	0.0130950020726	-0.234319041105	0.0261618072158	-0.0400151077816	0.0186359867258	0.142928822554	0.0484486026802	0.213632612477	-0.0178280061997	0.0353931511081	0.217543196631	-0.0191858707778	0.14409371938	25.7340986513	-22.8265141021	5.37311253939
5	1.14360107719	0.424522292793	-0.175586190295	2.46607628306	-0.615355255444	3.11485815464	-0.0454084246548	-0.160147536611	0.148656934101	0.165188672761	0.0342255963686	0.0875532920128	-0.262175162872	-0.0240048071096	0.0094374316365	0.163994579437	0.0245528604984	-0.0115603373704	0.169460078132	-0.0195358604798	0.202753022993	-13.6753308087	-10.352521813	8.60259762124
6	0.901495782048	0.170744767033	0.0427381458592	2.4380943799	0.766288132138	2.60209635965	-0.160495100269	0.24778164823	0.019630224646	-0.591777051612	0.112504856031	-0.0643218892607	-0.0872812777108	0.186829057307	0.0468298826455	0.319101847421	-0.0518332679977	-0.0144485409267	0.210169678751	0.016536775064	0.189733596842	-9.47030556885	-18.8926623281	-15.1522536641
7	1.49376288093	-0.467620829006	-0.367907209566	5.57590493625	-0.481845623482	3.13691390138	-0.00747058173759	-0.211685296005	-0.20704718117	0.626028591163	-0.0278097972648	0.195133679013	0.207255266514	-0.0988836221269	0.0433934253323	0.297207285123	-0.0290309403116	-0.0264917630015	0.202090555186	0.0242502871782	0.213681954007	-22.4312045463	12.3186753435	46.9693689047
8	0.875618885358	0.838748131412	-0.0894536006786	3.90062905896	-0.263571977307	2.20811322943	0.0287258255437	0.0491397733252	-0.110679225671	-0.0309554880912	-0.025369221298	-0.0229311793178	0.127046882686	-0.0402547466926	-0.0073439976668	0.169565177629	0.00133268405442	-0.00914896712863	0.146535186044	-0.0163391801579	0.157560782749	-20.8744640173	11.9728484594	28.8031535172
9	7.45606723068	-0.701519801868	0.95572764215	4.88073685994	2.08884493899	8.61205031331	-0.0299319560392	0.640652701739	-0.2153150156	-0.828975831266	-0.0786649104183	0.295835124047	0.482768462578	-0.727013780988	0.0959904636975	0.502853519731	-0.0498975681204	-0.00776868671042	0.314710352165	0.00331661836449	0.174925566394	-22.6992528527	21.7309380774	8.11697945817
10	3.04296616055	-1.09469450523	-1.57289445961	4.46072240602	1.39286823581	5.46653592516	0.016048609071	-0.14101340158	-0.108555183286	0.491773485264	0.00899427435182	0.121283151772	0.287921482764	-0.0920671814771	-0.0150452255924	0.269935178052	-0.0291598863674	-0.0293669655824	0.149301250195	0.0137161656893	0.165302151242	12.0485699475	9.37805838834	14.4566748947
11	1.26689221652	0.0287334934563	0.00487759164906	2.88990269266	-0.586560490901	3.07691385447	-0.0649842504557	-0.0756690263989	-0.0403926820273	0.404429117286	0.0312589747312	-0.072027532846	-0.116827633495	0.0711076224639	0.0332737052774	0.203854392766	0.0104379062699	-0.022648220366	0.151149917413	-0.00546607814398	0.175341668899	15.4713043683	13.7563802384	9.23183870241
12	0.647503582802	0.49721406272	0.239438023851	3.48764155005	-1.6841354614	4.31327765146	0.0403499083935	0.18650780698	-0.0785616204526	-0.121660869193	-0.0156116417489	0.0386360020497	0.286174701954	0.177009565765	-0.0660666046107	0.168366275225	0.00156372410913	-0.00950954361993	0.125533633487	-0.0461937177537	0.167535164081	12.1197571958	6.70899530843	-7.61538975707
13	0.661954839535	-0.181103704289	0.508185076175	3.61986232713	-0.692568775241	3.46814595547	-0.0694510449044	0.0553599869471	-1.2248904804E-6	0.0324839822603	0.0205902505683	0.0995866208715	-0.186353047583	-0.0363028767857	0.0628167755081	0.141013287977	-0.0140151462381	-0.0074557218916	0.162237685337	-0.0185762253961	0.159709599903	13.1399218082	16.916488761	-5.74471830723
14	3.46280417229	0.367990888863	0.484824367544	2.92799023685	-0.426286419099	4.40804324392	-0.0152401306105	0.238965246433	-0.0210134299291	-0.313513832499	-0.00540391812143	0.0370560183991	-0.0629353178801	0.0137005527465	0.0271340694592	0.287315876451	-0.0267362399101	-0.0666387811678	0.223677054384	0.00736466607786	0.201027234395	8.7687540292	21.6825910081	-26.4705128705

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 53 )	A	A	3 - 53	1 - 51
2	2	chain 'A' and (resid 54 through 141 )	A	A	54 - 141	52 - 139
3	3	chain 'A' and (resid 142 through 215 )	A	A	142 - 215	140 - 209
4	4	chain 'A' and (resid 216 through 277 )	A	A	216 - 277	210 - 271
5	5	chain 'B' and (resid 3 through 118 )	B	C	3 - 118	1 - 116
6	6	chain 'B' and (resid 119 through 274 )	B	C	119 - 274	117 - 266
7	7	chain 'C' and (resid 3 through 79 )	C	E	3 - 79	1 - 77
8	8	chain 'C' and (resid 80 through 215 )	C	E	80 - 215	78 - 209
9	9	chain 'C' and (resid 216 through 266 )	C	E	216 - 266	210 - 260
10	10	chain 'D' and (resid 3 through 54 )	D	G	3 - 54	1 - 52
11	11	chain 'D' and (resid 55 through 97 )	D	G	55 - 97	53 - 95
12	12	chain 'D' and (resid 98 through 141 )	D	G	98 - 141	96 - 139
13	13	chain 'D' and (resid 142 through 215 )	D	G	142 - 215	140 - 207
14	14	chain 'D' and (resid 216 through 277 )	D	G	216 - 277	208 - 269

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Jul 12, 2017. Major update of PDB

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Yorodumi