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

ID or keywords:

Entry

Database: PDB / ID: 5vct

Title

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

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 /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 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
Authors: Abendroth, J. / Higgins, T.W. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Mar 31, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	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	5vct.cif.gz	134.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5vct.ent.gz	102.4 KB	Display	PDB format
PDBx/mmJSON format	5vct.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	5j49S S: Starting model for refinement
Similar structure data	6b91-d 4dii-d 1dew-1 5i1f-d 2hpq-d 3own-2 3itm-4 3nfz-d 2bco-1 5zt1-2 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

33.5 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)	63.900, 111.210, 124.750
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-481- HOH
2	1	A-533- 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-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.33 Å³/Da / Density % sol: 63.12 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Optimization screen around RigakuReagents JCSG B9: 100mM Sodium citrate / citric acid pH 5.36, 19.8% PEG 6000, BuamA.00118.a.B1.PS37963 at 45.5 mg/ml, tray 289281 g6: cryo: 25% EG in 2 steps: puck obr5-7.

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2017

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.9→39.759 Å / Num. obs: 35235 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.013 % / B_iso Wilson estimate: 31.19 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.055 / R_rim(I) all: 0.062 / Χ²: 1.017 / Net I/σ(I): 15.81

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
1.9-1.95	5.138	0.484	3.12	2564	0.864	0.541	99.9
1.95-2	5.134	0.349	4.27	2510	0.925	0.39	99.9
2-2.06	5.097	0.265	5.66	2454	0.952	0.297	99.8
2.06-2.12	5.098	0.206	7.38	2389	0.969	0.23	99.6
2.12-2.19	5.061	0.158	9.07	2293	0.981	0.177	99.9
2.19-2.27	5.061	0.124	11.16	2226	0.987	0.138	99.4
2.27-2.36	5.067	0.105	13.09	2162	0.989	0.118	99.4
2.36-2.45	5.067	0.09	15.05	2052	0.991	0.1	99.1
2.45-2.56	5.053	0.078	17.02	2007	0.994	0.087	99.5
2.56-2.69	5.031	0.072	18.62	1888	0.994	0.08	99.5
2.69-2.83	5.033	0.063	20.95	1827	0.995	0.07	99.6
2.83-3	4.966	0.056	22.96	1727	0.996	0.063	99.4
3-3.21	4.894	0.053	24.51	1630	0.996	0.06	99.7
3.21-3.47	4.888	0.048	26.92	1523	0.997	0.054	99.8
3.47-3.8	4.852	0.047	28.13	1402	0.997	0.052	99.7
3.8-4.25	4.873	0.043	29.02	1295	0.997	0.048	100
4.25-4.91	4.863	0.04	29.81	1128	0.997	0.045	99.8
4.91-6.01	4.917	0.039	29.62	976	0.998	0.043	99.8
6.01-8.5	4.738	0.038	29.3	768	0.998	0.042	99.5
8.5-50	4.292	0.038	28.44	414	0.996	0.043	90.4

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5j49

5j49

Resolution: 1.9→39.759 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.11

	R_factor	Num. reflection	% reflection
R_free	0.1964	1959	5.56 %
R_work	0.1682	-	-
obs	0.1698	35227	99.52 %

Solvent computation

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

Displacement parameters

B_iso max: 111.55 Å² / B_iso mean: 40.6828 Å² / B_iso min: 17.81 Å²

Refinement step

Cycle: final / Resolution: 1.9→39.759 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2141	0	13	237	2391
B_iso mean	-	-	94.63	48.25	-
Num. residues	-	-	-	-	282

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2277
X-RAY DIFFRACTION	f_angle_d	0.854	3115
X-RAY DIFFRACTION	f_chiral_restr	0.056	360
X-RAY DIFFRACTION	f_plane_restr	0.006	406
X-RAY DIFFRACTION	f_dihedral_angle_d	15.767	1409

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 (%)
1.9-1.9476	0.2632	133	0.2407	2358	2491	100
1.9476-2.0002	0.2583	142	0.2209	2317	2459	100
2.0002-2.0591	0.2227	140	0.2074	2358	2498	100
2.0591-2.1255	0.2274	161	0.1965	2352	2513	100
2.1255-2.2015	0.2243	128	0.1828	2356	2484	100
2.2015-2.2896	0.2166	121	0.1807	2378	2499	99
2.2896-2.3938	0.1945	143	0.1677	2327	2470	99
2.3938-2.52	0.1886	131	0.1697	2368	2499	100
2.52-2.6778	0.197	125	0.1755	2377	2502	99
2.6778-2.8846	0.2216	137	0.1788	2401	2538	100
2.8846-3.1747	0.1939	158	0.1729	2364	2522	99
3.1747-3.6338	0.1955	145	0.1654	2389	2534	100
3.6338-4.5772	0.1698	137	0.142	2439	2576	100
4.5772-39.7681	0.1828	158	0.1575	2484	2642	98

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	7.2136	4.5406	-2.3788	3.3999	-2.9386	4.7879	0.2514	-0.1978	-0.0973	0.1931	-0.3144	-0.4016	-0.0029	0.091	0.1385	0.1916	0.0533	0.0098	0.1663	-0.0178	0.2313	-27.6864	-16.8618	-13.1133
2	1.1216	2.3313	-0.0376	6.4928	0.5801	0.3686	0.0653	0.0575	-0.1	-0.2988	-0.0554	-0.1336	-0.1061	-0.0435	-0.0036	0.2828	0.0438	0.0196	0.2306	-0.0128	0.2156	-32.2992	-8.1644	-17.0895
3	6.7107	-0.3731	2.3768	5.9554	1.5302	5.1852	-0.0785	-0.0834	0.3424	0.332	-0.103	-0.1994	-0.2803	-0.0986	0.1775	0.2111	0.0158	0.0165	0.2096	0.0158	0.141	-33.065	-12.2377	-7.0896
4	6.9179	-4.2499	2.6548	3.0961	-0.4803	5.7329	-0.3725	-0.6005	0.1315	0.5734	0.2315	1.0742	-0.5897	-1.071	0.173	0.4086	0.1245	0.042	0.5035	0.0094	0.5757	-49.2225	-4.5572	-9.3143
5	2.627	-2.7098	-1.4141	4.8697	0.7271	6.543	-0.0937	-0.4298	-0.0995	0.477	0.1781	-0.1581	0.1525	0.4023	-0.0918	0.2819	-0.0102	-0.0431	0.1915	-0.0053	0.2432	-27.4757	-18.9679	-5.0017
6	3.5293	-0.0812	-1.0591	1.516	0.4142	2.2409	-0.02	0.2035	-0.2299	-0.0751	0.0103	-0.0272	0.1563	-0.1423	0.0217	0.2512	0.0086	-0.0281	0.1769	-0.0685	0.2322	-27.4698	-25.0773	-22.9923
7	2.2472	-1.3083	-0.5696	3.5618	-1.5682	5.9114	-0.0727	-0.0293	-0.8481	-0.5163	0.0692	-0.0323	0.6101	-0.2173	-0.0067	0.4116	0.051	0.0227	0.2948	-0.1381	0.4371	-19.8929	-33.0797	-27.653
8	3.6573	-0.1764	-2.1669	0.9908	0.4358	2.4691	0.0193	-0.1753	-0.279	0.0976	0.0682	-0.2047	0.0655	0.2517	-0.0333	0.2794	0.0253	-0.0489	0.209	-0.052	0.3123	-17.6377	-26.8526	-19.5214
9	3.5721	-1.6688	0.9057	6.8409	-2.0493	3.2582	-0.0151	-0.0235	-0.1785	0.2357	-0.0714	-0.5118	0.0436	0.2915	0.0843	0.2375	0.0322	0.0424	0.2789	-0.056	0.2758	-20.4394	-25.859	-20.3915
10	5.681	-0.4341	1.0283	4.5511	-1.206	5.333	0.2059	0.6513	-0.0182	-1.0912	-0.4227	0.5425	0.4656	-0.3262	0.2068	0.5836	0.1258	-0.0865	0.4104	-0.077	0.252	-36.3327	-2.2998	-33.3209

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 18 )	A	2 - 18
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 48 )	A	19 - 48
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 68 )	A	49 - 68
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 69 through 94 )	A	69 - 94
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 95 through 122 )	A	95 - 122
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 123 through 171 )	A	123 - 171
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 172 through 191 )	A	172 - 191
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 192 through 220 )	A	192 - 220
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 221 through 258 )	A	221 - 258
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 259 through 287 )	A	259 - 287

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