PDB-9o90: Crystal structure of UTP--glucose-1-phosphate uridylyltransferase...

ID or keywords:

Entry

Database: PDB / ID: 9o90

Title

Crystal structure of UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis

Components

UTP--glucose-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Bordetella pertussis

Function / homology

UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases / GLYCINE / UTP--glucose-1-phosphate uridylyltransferase

Function and homology information

Biological species

Bordetella pertussis Tohama I (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.93 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal structure of UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis
Authors: Liu, L. / Lovell, S. / Seibold, S. / Battaile, K.P.

History

Deposition	Apr 17, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9o90.cif.gz	229.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9o90.ent.gz	183.6 KB	Display	PDB format
PDBx/mmJSON format	9o90.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9o90_validation.pdf.gz	466.8 KB	Display	wwPDB validaton report
Full document	9o90_full_validation.pdf.gz	470.3 KB	Display
Data in XML	9o90_validation.xml.gz	27.9 KB	Display
Data in CIF	9o90_validation.cif.gz	37.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/9o90 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/9o90	HTTPS FTP

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Related structure data

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 (2) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

Deposited unit

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

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

1

A: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

B: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

defined by author&software
Evidence: gel filtration
62.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.848, 94.336, 80.541
Angle α, β, γ (deg.)	90.00, 109.80, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-620- HOH

#1: Protein	UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase Mass: 30991.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella pertussis Tohama I (bacteria) Gene: BP3403 / Plasmid: BopeA.00118.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7VTV0, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₅NO₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 280 / 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: 3.34 Å³/Da / Density % sol: 63.18 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus H5: 20% PEG 550 MME, 10% PEG 20K, 0.1M HEPES/MOPS, pH 7.5, 20mM each of DL-Alanine, Glycine, DL-Lysine, DL-Serine, DL-Glutamic acid. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate ...Details: Morpheus H5: 20% PEG 550 MME, 10% PEG 20K, 0.1M HEPES/MOPS, pH 7.5, 20mM each of DL-Alanine, Glycine, DL-Lysine, DL-Serine, DL-Glutamic acid. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate 19783 H5 drop 1, Puck: PSL-1103, Cryo: direct.

Crystal

Density Matthews: 3.34 Å³/Da / Density % sol: 63.18 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus H5: 20% PEG 550 MME, 10% PEG 20K, 0.1M HEPES/MOPS, pH 7.5, 20mM each of DL-Alanine, Glycine, DL-Lysine, DL-Serine, DL-Glutamic acid. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 15, 2025
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.93→47.17 Å / Num. obs: 61154 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC_1/2: 0.995 / R_merge(I) obs: 0.183 / R_pim(I) all: 0.076 / R_rim(I) all: 0.198 / Χ²: 1.04 / Net I/σ(I): 9.3 / Num. measured all: 417462
Reflection shell	Resolution: 1.93→1.98 Å / % possible obs: 99.9 % / Redundancy: 7 % / R_merge(I) obs: 1.321 / Num. measured all: 31316 / Num. unique obs: 4464 / CC_1/2: 0.524 / R_pim(I) all: 0.535 / R_rim(I) all: 1.426 / Χ²: 0.92 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	1.21rc1_5156	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.93→47.17 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2148	2994	4.9 %
R_work	0.1843	-	-
obs	0.1858	61137	99.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.93→47.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4174	0	38	280	4492

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	4312
X-RAY DIFFRACTION	f_angle_d	1.042	5862
X-RAY DIFFRACTION	f_dihedral_angle_d	11.892	1607
X-RAY DIFFRACTION	f_chiral_restr	0.057	687
X-RAY DIFFRACTION	f_plane_restr	0.016	769

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 (%)
1.93-1.96	0.31	146	0.2989	2765	X-RAY DIFFRACTION	100
1.96-2	0.307	125	0.2957	2754	X-RAY DIFFRACTION	100
2-2.03	0.3253	135	0.2752	2750	X-RAY DIFFRACTION	100
2.03-2.07	0.3114	132	0.2663	2800	X-RAY DIFFRACTION	100
2.07-2.11	0.2821	153	0.2467	2726	X-RAY DIFFRACTION	100
2.11-2.16	0.2702	135	0.2338	2754	X-RAY DIFFRACTION	100
2.16-2.21	0.2467	136	0.216	2790	X-RAY DIFFRACTION	100
2.21-2.26	0.2774	150	0.2077	2735	X-RAY DIFFRACTION	100
2.26-2.33	0.2406	137	0.2001	2758	X-RAY DIFFRACTION	100
2.33-2.39	0.2438	166	0.1847	2742	X-RAY DIFFRACTION	100
2.39-2.47	0.2304	151	0.1835	2765	X-RAY DIFFRACTION	100
2.47-2.56	0.2504	141	0.1871	2771	X-RAY DIFFRACTION	100
2.56-2.66	0.2509	128	0.1909	2778	X-RAY DIFFRACTION	100
2.66-2.78	0.2507	147	0.1989	2774	X-RAY DIFFRACTION	100
2.78-2.93	0.1959	139	0.1825	2764	X-RAY DIFFRACTION	100
2.93-3.11	0.2111	164	0.1899	2777	X-RAY DIFFRACTION	100
3.11-3.35	0.215	119	0.1917	2783	X-RAY DIFFRACTION	100
3.35-3.69	0.1978	140	0.1676	2758	X-RAY DIFFRACTION	100
3.69-4.23	0.1593	146	0.154	2779	X-RAY DIFFRACTION	100
4.23-5.32	0.1618	149	0.1359	2793	X-RAY DIFFRACTION	99
5.32-47.17	0.202	155	0.169	2827	X-RAY DIFFRACTION	100

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	0.9203	-0.264	-0.2225	0.0562	0.1452	0.2181	0.0622	-0.1145	0.0102	0.0908	-0.0514	-0.0168	0.0022	-0.0778	-0	0.2754	-0.0173	0.0183	0.2309	-0.002	0.2473	47.026	-2.383	15.71
2	1.1129	-0.3586	0.0134	1.6071	0.1775	0.7291	-0.0377	0.1097	-0.0783	-0.0392	0.0334	-0.115	0.1467	-0.1505	-0.0009	0.2113	-0.0158	-0.0033	0.2149	0.0189	0.2202	39.223	-2.962	15.823
3	0.3486	-0.4574	0.0015	1.1348	0.4526	0.2939	0.0513	0.0907	0.0974	-0.1524	-0.0927	-0.2886	-0.4412	-0.1012	-0.005	0.3282	0.1034	0.0061	0.3399	0.0316	0.2583	31.827	11.762	17.525
4	0.851	0.1221	-0.6177	0.2425	0.0677	0.8085	-0.0082	-0.1825	-0.0555	0.0593	0.0277	0.0036	0.0701	-0.0771	0.0005	0.2684	0.017	0.0123	0.2293	0.0056	0.2526	44.144	-1.832	28.721
5	0.6629	0.0567	-0.0735	0.0578	-0.1891	0.4316	-0.0508	-0.4978	-0.2313	0.0385	0.0996	0.0431	0.1571	-0.0009	-0.0015	0.2916	-0.0332	0.0156	0.2233	-0.0323	0.2873	45.595	-8.793	-13.118
6	0.8267	0.6338	-0.348	0.4806	-0.251	0.1689	-0.014	0.1358	-0.0437	-0.1059	-0.0762	-0.0151	0.0003	0.1275	-0	0.2705	-0.0088	0.0027	0.2469	0.0049	0.232	45.408	-1.84	-14.601
7	0.6264	0.1908	0.156	0.1199	0.1736	0.3222	0.032	-0.2911	0.4206	0.7382	0.0881	-0.4113	-0.2961	-0.0537	0.068	0.3551	-0.0499	-0.0244	0.2274	-0.0677	0.4245	54.493	7.786	-6.638
8	0.3585	0.088	0.2097	0.1631	0.3276	0.6439	0.1729	-0.1987	0.1057	-0.1845	-0.1837	-0.0214	-0.0304	0.0883	-0.0003	0.3258	0.0295	0.027	0.2122	-0.01	0.2803	45.563	2.684	-8.574
9	0.8302	0.489	0.54	0.7211	0.4927	0.4174	-0.0201	-0.0603	0.1604	-0.0221	-0.0162	0.1297	-0.0747	-0.2789	0	0.2608	0.0029	-0.0105	0.3131	0.0185	0.289	33.15	-5.619	-16.011
10	0.3619	-0.1733	-0.0709	0.5663	-0.112	0.5602	0.0546	0.0739	0.1013	-0.5109	0.1257	0.0817	-0.3835	-0.046	0.0068	0.2669	-0.1089	0.0098	0.3495	-0.0155	0.3049	34.304	-16.263	-28.423
11	1.3855	-0.0168	-0.938	0.2969	-0.0117	1.2737	-0.3107	0.3049	-0.2591	-0.3422	0.1278	0.3443	0.2607	-0.0991	-0.3462	0.3174	-0.1393	-0.1054	0.342	-0.0041	0.3037	27.481	-18.601	-27.734
12	0.0797	0.1149	0.0205	0.1505	0.0205	0.0066	-0.009	0.1505	0.0818	-0.2529	0.0257	0.1761	0.1019	-0.3915	0.0001	0.2958	-0.1009	-0.0171	0.3776	-0.0126	0.2816	31.802	-13.617	-23.032
13	0.3681	0.2538	0.5073	0.172	0.3466	0.6833	0.3379	-0.1572	-0.2953	0.0825	0.052	0.2024	0.7723	-0.1456	0.0647	0.4724	-0.1825	-0.0772	0.3931	0.0259	0.3405	29.653	-19.726	-10.834
14	0.2083	0.2024	-0.1239	1.1925	0.0091	0.2323	-0.1093	0.189	-0.0252	-0.4313	0.1085	0.1632	0.2422	-0.1674	-0.0519	0.3809	-0.1112	-0.1069	0.3658	0.0473	0.2724	33.004	-9.526	-24.7
15	0.37	0.0331	0.2197	0.0663	-0.0344	0.1737	-0.0078	0.1382	-0.0954	-0.3371	-0.001	-0.0624	0.2081	0.217	-0	0.4065	-0.0017	0.04	0.2839	0.0139	0.2705	53.557	-0.91	-31.718
16	0.095	0.0549	-0.0476	0.0514	0.0072	0.0544	0.1862	0.0288	-0.3605	0.0082	-0.0193	0.2102	-0.154	0.1685	-0.0001	0.6913	0.1152	-0.0676	0.6732	-0.2497	0.9603	44.387	-3.67	-0.058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 2:47 )	A	2 - 47
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 48:191 )	A	48 - 191
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 192:240 )	A	192 - 240
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 241:279 )	A	241 - 279
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 1:26 )	B	1 - 26
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 27:60 )	B	27 - 60
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 61:83 )	B	61 - 83
8	X-RAY DIFFRACTION	8	( CHAIN B AND RESID 84:110 )	B	84 - 110
9	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 111:153 )	B	111 - 153
10	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 154:171 )	B	154 - 171
11	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 172:197 )	B	172 - 197
12	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 198:211 )	B	198 - 211
13	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 212:240 )	B	212 - 240
14	X-RAY DIFFRACTION	14	( CHAIN B AND RESID 241:258 )	B	241 - 258
15	X-RAY DIFFRACTION	15	( CHAIN B AND RESID 259:279 )	B	259 - 279
16	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 301:302 ) OR ( CHAIN B AND RESID 301:302 )	A	301 - 302
17	X-RAY DIFFRACTION	16	( CHAIN A AND RESID 301:302 ) OR ( CHAIN B AND RESID 301:302 )	B	301 - 302

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