PDB-5j49: Crystal structure of UDP-glucose pyrophosporylase / UTP-glucose-1...

ID or keywords:

Entry

Database: PDB / ID: 5j49

Title

Crystal structure of UDP-glucose pyrophosporylase / UTP-glucose-1-phosphate uridylyltransferase from Burkholderia xenovorans

Components

UTP--glucose-1-phosphate uridylyltransferase

Keywords

TRANSFERASE / SSGCID / Burkholderia xenovorans / UTP-glucose-1-phosphate uridylyltransferase / UTP-glucose / uridylyltransferase / 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 xenovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal structure of UDP-glucose pyrophosporylase / UTP-glucose-1-phosphate uridylyltransferase from Burkholderia xenovorans
Authors: Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edewards, T.E.

History

Deposition	Mar 31, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 4, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5j49.cif.gz	250.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5j49_validation.pdf.gz	457.2 KB	Display	wwPDB validaton report
Full document	5j49_full_validation.pdf.gz	459.6 KB	Display
Data in XML	5j49_validation.xml.gz	26.5 KB	Display
Data in CIF	5j49_validation.cif.gz	39.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j4/5j49 ftp://data.pdbj.org/pub/pdb/validation_reports/j4/5j49	HTTPS FTP

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Related structure data

Related structure data	3jujS S: Starting model for refinement
Similar structure data	2ux8-1 2e3d-d 6mnu-d 6ikz-1 1nqk-1 3fwp-d 6kkr-d 6k8d-d Search similar-shape structures by Omokage search (details) 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: BuxeA.00118.c

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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

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

1

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

A: UTP--glucose-1-phosphate uridylyltransferase

B: UTP--glucose-1-phosphate uridylyltransferase

hetero molecules

defined by author&software
135 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	134.110, 134.110, 73.150
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-607- HOH

#1: Protein	UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase Mass: 33409.473 Da / Num. of mol.: 2 / Fragment: BuxeA.00118.c.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria) Strain: LB400 / Gene: Bxe_A1334 / Plasmid: BuxeA.00118.c.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q13WC0, UTP-glucose-1-phosphate uridylyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.46 Å³/Da / Density % sol: 50 % / Mosaicity: 0.15 °
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Microlytic MCSG1 screen H7: 2M Ammonium sulphate, 100mM BisTris pH 5.5; BuxeA.00118.c.B1.PS02592 at 16mg/ml; cryo: 25% EG in two steps; tray 269868 h7, puck RPA3-4

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 3, 2016

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 62217 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / B_iso Wilson estimate: 22.63 Å² / CC_1/2: 1 / R_merge(I) obs: 0.051 / Net I/σ(I): 33.26

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.8-1.85	0.53	5.27	1	100
1.85-1.9	0.425	6.59	1	100
1.9-1.95	0.328	8.57	1	100
1.95-2.01	0.256	10.83	1	100
2.01-2.08	0.191	14.09	1	100
2.08-2.15	0.16	16.75	1	100
2.15-2.23	0.127	20.46	1	100
2.23-2.32	0.104	24.4	1	100
2.32-2.43	0.087	28.58	1	100
2.43-2.55	0.076	32.11	1	100
2.55-2.68	0.064	36.55	1	100
2.68-2.85	0.054	42.78	1	100
2.85-3.04	0.045	50.79	1	100
3.04-3.29	0.037	59.98	1	100
3.29-3.6	0.029	72.84	1	100
3.6-4.02	0.027	80.77	1	100
4.02-4.65	0.024	87.86	1	100
4.65-5.69	0.022	89.26	1	100
5.69-8.05	0.023	84.55	1	100
8.05-50	0.02	89.54	1	97.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3juj

3juj

Resolution: 1.8→50 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.16

	R_factor	Num. reflection	% reflection
R_free	0.2071	1953	3.14 %
R_work	0.1706	-	-
obs	0.1717	62144	99.97 %

Solvent computation

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

Displacement parameters

B_iso max: 99.88 Å² / B_iso mean: 33.3583 Å² / B_iso min: 12.01 Å²

Refinement step

Cycle: final / Resolution: 1.8→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4437	0	29	433	4899
B_iso mean	-	-	62.63	40.13	-
Num. residues	-	-	-	-	584

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4637
X-RAY DIFFRACTION	f_angle_d	0.862	6324
X-RAY DIFFRACTION	f_chiral_restr	0.056	719
X-RAY DIFFRACTION	f_plane_restr	0.005	822
X-RAY DIFFRACTION	f_dihedral_angle_d	14.302	2820

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 (%)
1.8-1.845	0.2262	135	0.2017	4237	X-RAY DIFFRACTION	100
1.845-1.8949	0.2124	143	0.1894	4252	X-RAY DIFFRACTION	100
1.8949-1.9507	0.2265	151	0.183	4199	X-RAY DIFFRACTION	100
1.9507-2.0137	0.2145	145	0.1862	4257	X-RAY DIFFRACTION	100
2.0137-2.0856	0.2188	139	0.1823	4236	X-RAY DIFFRACTION	100
2.0856-2.1691	0.2327	130	0.1828	4243	X-RAY DIFFRACTION	100
2.1691-2.2678	0.2597	138	0.1789	4274	X-RAY DIFFRACTION	100
2.2678-2.3874	0.1986	166	0.1764	4246	X-RAY DIFFRACTION	100
2.3874-2.537	0.252	138	0.1759	4281	X-RAY DIFFRACTION	100
2.537-2.7328	0.2237	133	0.1792	4311	X-RAY DIFFRACTION	100
2.7328-3.0078	0.2199	122	0.179	4325	X-RAY DIFFRACTION	100
3.0078-3.4429	0.2161	130	0.1683	4347	X-RAY DIFFRACTION	100
3.4429-4.3373	0.15	139	0.1482	4401	X-RAY DIFFRACTION	100
4.3373-49	0.2027	144	0.1629	4582	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	3.2948	-1.6273	-0.1716	2.145	-0.4992	0.9338	0.0816	0.0982	0.1033	-0.169	-0.0814	-0.0856	-0.131	0.0177	-0.0083	0.1901	-0.0302	0.0688	0.1252	-0.022	0.1636	43.6369	58.4377	-2.5254
2	3.469	0.7539	0.6584	2.6125	-0.0233	1.43	0.0838	-0.2541	-0.1815	0.1011	0.1042	-0.0535	0.0209	-0.0542	-0.2156	0.1708	0.01	0.0529	0.1533	-0.0442	0.1575	36.8025	55.9801	1.8844
3	3.6688	0.787	0.2645	2.1429	-0.7465	2.9294	-0.2027	0.5882	0.2846	-0.6697	0.2251	0.0845	-0.3752	0.0237	-0.0745	0.4917	-0.06	0.039	0.2265	0.0548	0.2621	36.8588	72.8348	-15.7996
4	2.6138	-1.3431	0.6431	2.2402	-0.7043	0.8989	-0.1221	-0.0005	0.5177	-0.1267	0.1101	-0.4745	-0.2782	0.1051	-0.0135	0.3046	-0.0747	0.0987	0.1995	-0.0621	0.3002	52.6616	67.7212	-4.1011
5	3.6608	-1.684	0.9256	7.9182	-3.2208	5.6997	-0.198	-0.1974	0.3013	0.6038	0.0084	-0.1237	-0.273	0.1757	0.1873	0.0955	-0.0009	0.0159	0.1245	-0.0185	0.1268	19.3679	42.2429	2.9414
6	2.0351	-1.4534	0.4842	2.1461	-0.8827	1.0091	-0.0427	-0.0365	-0.207	-0.0429	-0.0017	0.1484	-0.0512	0.0153	0.0447	0.1129	-0.0172	0.0107	0.1349	0.0065	0.1578	22.1468	33.6084	-1.2309
7	6.9057	-0.4355	-0.2175	3.9153	2.3445	2.2257	-0.0058	-0.1194	0.0198	0.0804	0.1084	-0.329	0.1714	0.2707	-0.0786	0.127	-0.0164	0.0266	0.1259	0.0098	0.1048	26.7902	42.8501	-1.7042
8	2.1832	-0.0826	-0.7875	5.0468	1.8463	3.6846	0.0244	0.2094	0.1002	-0.6763	0.201	-0.4564	0.0399	0.2877	-0.2749	0.2261	-0.0092	0.0045	0.1899	-0.006	0.1691	27.4258	42.599	-6.3742
9	2.5625	0.3114	0.293	2.5846	0.1433	2.0547	0.0511	-0.3867	0.2951	0.267	-0.089	0.3714	-0.0865	-0.2248	0.0312	0.1352	-0.0026	0.0195	0.2112	-0.0496	0.2314	5.7243	44.9379	8.264
10	2.475	-0.9771	-0.1022	2.0871	-0.0317	0.7525	-0.026	0.0716	-0.224	0.0572	-0.0843	0.2513	0.1154	-0.1046	0.0906	0.1281	-0.0505	-0.017	0.1729	-0.0052	0.1861	12.5044	23.598	-0.5249

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 48 )	A	2 - 48
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 141 )	A	49 - 141
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 142 through 230 )	A	142 - 230
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 231 through 293 )	A	231 - 293
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 18 )	B	2 - 18
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 19 through 48 )	B	19 - 48
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 49 through 68 )	B	49 - 68
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 69 through 122 )	B	69 - 122
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 123 through 240 )	B	123 - 240
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 241 through 293 )	B	241 - 293

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