PDB-9ygk: Crystal Structure UTP--glucose-1-phosphate uridylyltransferase fr...

ID or keywords:

Entry

Database: PDB / ID: 9ygk

Title

Crystal Structure UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound)

Components

UTP--glucose-1-phosphate uridylyltransferase

Keywords

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

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 / biosynthetic process / Nucleotide-diphospho-sugar transferases / UTP--glucose-1-phosphate uridylyltransferase

Function and homology information

Biological species

Bordetella pertussis Tohama I (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

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 UTP--glucose-1-phosphate uridylyltransferase from Bordetella pertussis (sulfate bound)
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.

History

Deposition	Sep 29, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 8, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ygk.cif.gz	229.1 KB	Display	PDBx/mmCIF format
PDB format	pdb9ygk.ent.gz	183.1 KB	Display	PDB format
PDBx/mmJSON format	9ygk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yg/9ygk ftp://data.pdbj.org/pub/pdb/validation_reports/yg/9ygk	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)

Deposited unit

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, dimeric

Unit cell

Length a, b, c (Å)	116.246, 95.799, 81.205
Angle α, β, γ (deg.)	90.00, 110.36, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-413- CL

#1: Protein	UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase Mass: 30991.625 Da / Num. of mol.: 2 / Fragment: 26-302 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-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.42 Å³/Da / Density % sol: 64.03 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Index B6: 0.1M HEPES pH 7.0, 1.4M Sodium citrate tribasic dihydrate. BopeA.00118.a.B2.PW39372 at 25.3 mg/mL. plate 19780 B6 drop 1, Puck: PSL-1201, Cryo: 2.5M Lithium Sulfate

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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: Apr 7, 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: 1.95→47.16 Å / Num. obs: 58027 / % possible obs: 95.6 % / Redundancy: 6.9 % / CC_1/2: 0.999 / R_merge(I) obs: 0.059 / R_pim(I) all: 0.024 / R_rim(I) all: 0.064 / Χ²: 0.83 / Net I/σ(I): 14 / Num. measured all: 400715
Reflection shell	Resolution: 1.95→2 Å / % possible obs: 98.4 % / Redundancy: 7.1 % / R_merge(I) obs: 1.004 / Num. measured all: 29919 / Num. unique obs: 4194 / CC_1/2: 0.833 / R_pim(I) all: 0.401 / R_rim(I) all: 1.082 / Χ²: 0.7 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	(2.0_5819: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.95→47.16 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2232	2895	4.99 %
R_work	0.1843	-	-
obs	0.1862	57968	95.34 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→47.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4103	0	116	229	4448

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.018	4293
X-RAY DIFFRACTION	f_angle_d	1.289	5856
X-RAY DIFFRACTION	f_dihedral_angle_d	13.13	1557
X-RAY DIFFRACTION	f_chiral_restr	0.087	680
X-RAY DIFFRACTION	f_plane_restr	0.012	749

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 (%)
1.95-1.98	0.3051	132	0.2533	2751	X-RAY DIFFRACTION	98
1.98-2.02	0.2833	135	0.2362	2664	X-RAY DIFFRACTION	98
2.02-2.05	0.3101	144	0.2332	2650	X-RAY DIFFRACTION	98
2.05-2.09	0.275	153	0.2365	2529	X-RAY DIFFRACTION	91
2.09-2.13	0.2891	139	0.2285	2646	X-RAY DIFFRACTION	98
2.14-2.18	0.2989	162	0.2214	2679	X-RAY DIFFRACTION	98
2.18-2.23	0.2628	149	0.2071	2677	X-RAY DIFFRACTION	99
2.23-2.29	0.2733	139	0.2002	2513	X-RAY DIFFRACTION	91
2.29-2.35	0.2412	134	0.1882	2693	X-RAY DIFFRACTION	99
2.35-2.42	0.2366	148	0.1868	2721	X-RAY DIFFRACTION	99
2.42-2.5	0.2468	146	0.187	2678	X-RAY DIFFRACTION	99
2.5-2.59	0.2547	131	0.1988	2731	X-RAY DIFFRACTION	99
2.59-2.69	0.2982	97	0.2164	2088	X-RAY DIFFRACTION	75
2.69-2.81	0.2587	150	0.2189	2707	X-RAY DIFFRACTION	99
2.81-2.96	0.2679	114	0.2189	2777	X-RAY DIFFRACTION	99
2.96-3.15	0.2716	131	0.2236	2757	X-RAY DIFFRACTION	99
3.15-3.39	0.2493	140	0.2083	2738	X-RAY DIFFRACTION	100
3.39-3.73	0.1824	113	0.1637	1986	X-RAY DIFFRACTION	73
3.73-4.27	0.1921	148	0.1498	2511	X-RAY DIFFRACTION	91
4.27-5.38	0.1551	150	0.1332	2755	X-RAY DIFFRACTION	99
5.38-47.16	0.2086	140	0.1795	2822	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	7.8212	-3.2061	0.6879	2.5785	0.2069	1.2399	0.1793	-0.142	0.2695	-0.0492	-0.0998	0.0503	-0.1153	0.0602	-0.0733	0.4614	-0.0113	0.039	0.3107	0.0303	0.3458	-1.3456	0.8135	24.8356
2	3.7336	1.4937	0.5365	1.4999	0.6109	3.9926	0.1496	-0.1949	-0.236	0.1638	-0.1411	0.0906	0.2714	-0.2274	0.0016	0.398	0.0393	-0.0026	0.2874	0.0213	0.3491	-1.3944	-7.4671	26.4951
3	1.6388	0.4285	0.3332	4.5088	-0.8599	3.9821	-0.0037	0.0671	0.0637	0.0996	-0.0152	0.1136	-0.0853	0.2209	0.0174	0.271	-0.0164	0.0127	0.4123	-0.0263	0.34	13.8421	8.0952	15.8986
4	8.4554	1.7675	-0.5436	2.105	-0.1008	0.2494	0.2547	0.5737	-0.4015	-0.0609	-0.059	0.03	-0.0193	0.0078	-0.182	0.3814	0.0689	-0.0005	0.4533	-0.0244	0.2597	-0.9852	-2.6318	9.1456
5	3.6495	2.6302	-1.1861	2.505	0.1427	1.9756	0.1102	-0.0999	-0.5033	0.0569	-0.1429	-0.1375	0.0264	0.0618	0.0421	0.4331	0.0204	-0.043	0.2769	0.0713	0.3534	-1.1268	-8.9255	51.1661
6	3.6031	-0.739	-1.1671	1.7072	0.6711	2.3459	0.0518	0.0035	-0.1164	-0.0192	-0.1451	0.0586	0.0655	-0.1065	0.0969	0.4223	-0.003	-0.0346	0.3221	0.0289	0.372	-2.7237	-2.1299	50.7436
7	2.3209	-1.4198	0.4122	1.9534	-0.9752	3.2384	0.0387	-0.0479	0.1683	0.0089	0.0608	-0.0318	-0.2817	-0.0856	-0.0988	0.3258	-0.0322	-0.0023	0.2663	-0.0058	0.3531	3.9253	-3.5197	53.0501
8	2.234	1.359	-0.6551	2.977	-0.1383	2.4685	-0.1465	-0.2866	-0.1058	0.2917	-0.1898	-0.243	-0.0161	0.2602	0.251	0.3818	0.0594	-0.0342	0.5596	0.0362	0.4626	16.0991	-19.3922	65.7367
9	0.254	-0.755	0.3272	3.3903	-0.5301	1.3238	-0.1288	-0.3106	-0.0338	0.4166	0.0788	0.0036	-0.1086	0.0747	0.1044	0.3851	0.0416	-0.0752	0.5033	0.0336	0.4342	11.9957	-14.134	60.9635
10	9.5271	-1.1173	0.6697	2.3824	-4.3276	8.3827	0.4415	0.1269	-0.6988	-0.396	-0.303	-0.5168	1.4698	0.7334	-0.1828	0.6328	0.0885	-0.0848	0.3747	-0.0269	0.5423	15.4908	-19.7741	48.5008
11	6.9559	-2.0981	0.0638	1.9136	0.2805	0.2314	0.1984	-0.4876	-0.0329	0.1506	0.0231	-0.0876	0.1534	0.0412	-0.2088	0.4304	-0.0415	-0.0526	0.4412	0.0548	0.3199	0.6301	-5.7787	66.3329

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 49 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 50 through 164 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 264 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 265 through 302 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 24 through 49 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 50 through 91 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 92 through 194 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 195 through 220 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 221 through 234 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 235 through 263 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 264 through 302 )

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