PDB-5ve7: Crystal structure of UTP-glucose-1-phosphate uridylyltransferase ...

ID or keywords:

Entry

Database: PDB / ID: 5ve7

Title

Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP

Components

UTP--glucose-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / SSGCID /

Burkholderia ambifaria /

UTP-glucose-1-phosphate uridylyltransferase / UTP / alpha-D-glucose / 1-phosphate / diphosphate /

UDP-glucose /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process
Similarity search - Function

Biological species

Burkholderia ambifaria (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of UTP-glucose-1-phosphate uridylyltransferase from Burkholderia ambifaria in complex with UTP
Authors: Abendroth, J. / Higgins, T.W. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.

History

Deposition	Apr 4, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2017	Group: Advisory / Category: database_PDB_caveat
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5ve7.cif.gz	132.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ve7.ent.gz	100.4 KB	Display	PDB format
PDBx/mmJSON format	5ve7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ve/5ve7 ftp://data.pdbj.org/pub/pdb/validation_reports/ve/5ve7	HTTPS FTP

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Related structure data

Related structure data	5vctS S: Starting model for refinement
Similar structure data	1sqd-d 4o2h-2 1eai-2 6nje-d 2i1y-2 3zjc-2 1tfz-d 5ywi-d 6jn7-1 2rj1-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: BuamA.00118.a

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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

hetero molecules

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

1

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

Unit cell

Length a, b, c (Å)	63.250, 108.480, 124.510
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	A-62- ARG
2	1	A-436- HOH

#1: Protein	UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase Mass: 33297.309 Da / Num. of mol.: 1 / Fragment: BuamA.00118.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria) Strain: MC40-6 / Gene: BamMC406_1359 / Plasmid: BuamA.00116.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B1YNX3, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical	ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₅N₂O₁₅P₃ / Comment: UTP*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.21 Å³/Da / Density % sol: 63.73 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.07 Details: Optimization screen around RigakuReagents JCSG B9: 100mM Sodium citrate / citric acid pH 5.07, 18.73% PEG 6000, BuamA.00118.a.B1.PS37963 at 45.5 mg/ml + 3mM GTP (BSI1746) + 3mM Glucose-1- ...Details: Optimization screen around RigakuReagents JCSG B9: 100mM Sodium citrate / citric acid pH 5.07, 18.73% PEG 6000, BuamA.00118.a.B1.PS37963 at 45.5 mg/ml + 3mM GTP (BSI1746) + 3mM Glucose-1-phosphate (BSI 1952) + 3mM MgCl2, tray 289280h3: cryo: 25% EG in 3 steps: puck kzj0-7.

Crystal

Density Matthews: 3.21 Å³/Da / Density % sol: 63.73 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.07
Details: Optimization screen around RigakuReagents JCSG B9: 100mM Sodium citrate / citric acid pH 5.07, 18.73% PEG 6000, BuamA.00118.a.B1.PS37963 at 45.5 mg/ml + 3mM GTP (BSI1746) + 3mM Glucose-1- ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 21, 2017

Radiation

Monochromator: RIKGAU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.3→50 Å / Num. obs: 19325 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 7.055 % / B_iso Wilson estimate: 31.88 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.069 / Χ²: 1.064 / Net I/σ(I): 20.79

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.3-2.36	7.159	0.308	7.51	1341	0.984	0.333	94.2
2.36-2.42	7.226	0.237	9.12	1374	0.988	0.255	99.6
2.42-2.49	7.209	0.196	10.71	1343	0.991	0.211	99.8
2.49-2.57	7.215	0.179	11.72	1295	0.991	0.194	99.6
2.57-2.66	7.216	0.155	13.01	1259	0.993	0.167	99.8
2.66-2.75	7.242	0.134	14.43	1235	0.995	0.145	99.9
2.75-2.85	7.245	0.118	16.15	1202	0.995	0.128	99.7
2.85-2.97	7.255	0.1	18.43	1123	0.996	0.108	99.9
2.97-3.1	7.241	0.088	20.15	1089	0.997	0.095	100
3.1-3.25	7.17	0.076	22.96	1048	0.997	0.083	99.8
3.25-3.43	7.096	0.071	24.87	1004	0.997	0.077	100
3.43-3.64	6.058	0.069	26.83	952	0.996	0.076	99.9
3.64-3.89	6.198	0.061	29.66	898	0.996	0.067	99.8
3.89-4.2	6.971	0.046	33.52	840	0.999	0.049	98.4
4.2-4.6	7.059	0.04	36.6	761	0.999	0.044	99.7
4.6-5.14	7.109	0.036	38.11	704	0.999	0.039	100
5.14-5.94	7.114	0.039	35.36	638	0.999	0.042	100
5.94-7.27	7.075	0.034	35.61	534	0.999	0.037	100
7.27-10.29	6.853	0.027	40.58	430	0.999	0.029	100
10.29-39.092	6.071	0.028	40.3	255	0.999	0.031	97.3

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: native structure, 5vct

5vct

Resolution: 2.3→39.092 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.03

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2213	1932	10 %	0, random
R_work	0.1775	-	-	-
obs	0.1817	19315	99.31 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 108.43 Å² / B_iso mean: 40.4692 Å² / B_iso min: 12.68 Å²

Refinement step

Cycle: final / Resolution: 2.3→39.092 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2149	0	29	198	2376
B_iso mean	-	-	30.14	43.84	-
Num. residues	-	-	-	-	282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2234
X-RAY DIFFRACTION	f_angle_d	0.892	3046
X-RAY DIFFRACTION	f_chiral_restr	0.053	353
X-RAY DIFFRACTION	f_plane_restr	0.006	397
X-RAY DIFFRACTION	f_dihedral_angle_d	13.953	1360

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3001-2.3576	0.3286	137	0.2752	1143	1280	94
2.3576-2.4213	0.3198	156	0.2253	1216	1372	100
2.4213-2.4926	0.2785	154	0.2005	1197	1351	100
2.4926-2.573	0.2536	130	0.2081	1237	1367	100
2.573-2.665	0.2744	133	0.2003	1241	1374	100
2.665-2.7716	0.3099	133	0.1943	1250	1383	100
2.7716-2.8977	0.2376	141	0.1855	1210	1351	100
2.8977-3.0505	0.2155	141	0.1931	1255	1396	100
3.0505-3.2415	0.2403	130	0.1821	1235	1365	100
3.2415-3.4916	0.2053	144	0.1763	1254	1398	100
3.4916-3.8427	0.2258	124	0.1778	1251	1375	100
3.8427-4.3981	0.1906	122	0.1476	1269	1391	99
4.3981-5.5387	0.1435	136	0.1324	1287	1423	100
5.5387-39.0975	0.201	151	0.1832	1338	1489	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	1.1745	0.955	-0.5875	3.1835	-0.3076	1.3701	0.0024	-0.0504	-0.1396	-0.3109	-0.0139	-0.1569	0.0879	0.101	0.0291	0.2492	0.0385	0.0038	0.2477	-0.0198	0.2244	-28.0721	-9.2817	-14.7084
2	1.6	-0.5496	1.7414	4.921	0.8967	4.3758	-0.147	-0.0215	0.0189	0.1518	0.0617	0.196	-0.2603	-0.1729	0.1506	0.1874	0.0498	0.0647	0.2422	0.0283	0.2021	-34.4673	-12.4124	-10.1783
3	2.8011	-2.8193	0.8026	6.194	-1.3487	1.7932	-0.8017	-0.6679	-0.0616	1.3807	1.4911	1.8062	-0.3671	-1.0857	-0.3842	0.5066	0.2029	0.1617	0.6963	0.2378	0.7184	-49.1268	-3.3	-9.2694
4	5.7815	0.4134	0.1221	5.6599	-0.5289	4.742	0.1078	-0.3777	-0.1239	0.307	-0.0648	0.0959	0.3558	0.2293	-0.0257	0.2708	0.0548	0.0199	0.2058	0.037	0.2607	-27.1311	-18.1807	-4.9514
5	3.6661	0.0198	-0.2303	1.0172	0.8525	1.608	-0.0064	0.0675	-0.3774	-0.0414	-0.0081	0.0491	0.2504	-0.1617	0.0264	0.294	0.006	-0.0303	0.1664	-0.044	0.2883	-27.4245	-24.8573	-22.5612
6	3.4072	4.8313	0.9733	8.4699	-0.3376	4.3259	0.0496	-0.3158	-0.8303	-0.4587	-0.2401	-0.0209	0.5977	-0.1749	0.1934	0.4333	0.1102	0.0875	0.3067	-0.1139	0.4996	-19.0936	-32.3253	-27.1979
7	4.1668	0.4134	-2.8944	2.0559	0.1478	2.9235	-0.0701	-0.4311	-0.5057	0.2576	-0.0718	-0.1251	0.1976	0.4612	0.1402	0.3437	0.0373	-0.0238	0.2929	-0.0039	0.3234	-17.4864	-26.2567	-19.2142
8	6.2742	1.1718	-1.6497	2.5128	3.4405	6.5964	0.338	0.1444	-0.4506	0.5435	0.0964	-1.2139	0.0476	0.4468	-0.5128	0.3991	0.1639	-0.0547	0.525	0.0459	0.5001	-13.3476	-27.6861	-13.7452
9	2.5166	-0.2789	-0.7124	7.1536	1.5743	1.7099	-0.1313	0.2842	-0.3986	-0.0062	0.2844	-0.0639	-0.1263	0.0082	-0.1089	0.2558	0.0158	0.0381	0.3068	-0.0714	0.2909	-26.1063	-22.757	-25.9064
10	6.8865	-1.1772	-0.2697	4.8123	-0.9886	6.116	0.1568	0.31	-0.1847	-1.1867	-0.1302	0.6252	-0.0261	-0.5184	0.0339	0.6041	0.0448	-0.0861	0.3608	-0.0704	0.2675	-35.5675	-2.2338	-32.7896

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 through 36 )	A	2 - 36
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 71 )	A	37 - 71
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 72 through 94 )	A	72 - 94
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 95 through 122 )	A	95 - 122
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 123 through 171 )	A	123 - 171
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 172 through 191 )	A	172 - 191
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 192 through 220 )	A	192 - 220
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 221 through 241 )	A	221 - 241
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 242 through 258 )	A	242 - 258
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 259 through 287 )	A	259 - 287

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