PDB-5ids: Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase ...

ID or keywords:

Entry

Database: PDB / ID: 5ids

Title

Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Burkholderia vietnamiensis

Components

Glucose-1-phosphate thymidylyltransferase

Keywords

TRANSFERASE / SSGCID / Glucose-1-phosphate thymidylyltransferase / Burkholderia vietnamiensis / Nucleotidyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

glucose-1-phosphate thymidylyltransferase / glucose-1-phosphate thymidylyltransferase activity / : / metal ion binding
Similarity search - Function

Biological species

Burkholderia vietnamiensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Burkholderia vietnamiensis
Authors: Dranow, D.M. / Hornayi, P.S. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Feb 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2	Sep 27, 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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Download

PDBx/mmCIF format	5ids.cif.gz	443 KB	Display	PDBx/mmCIF format
PDB format	pdb5ids.ent.gz	362.9 KB	Display	PDB format
PDBx/mmJSON format	5ids.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ids_validation.pdf.gz	454.5 KB	Display	wwPDB validaton report
Full document	5ids_full_validation.pdf.gz	461.4 KB	Display
Data in XML	5ids_validation.xml.gz	40.8 KB	Display
Data in CIF	5ids_validation.cif.gz	57.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/id/5ids ftp://data.pdbj.org/pub/pdb/validation_reports/id/5ids	HTTPS FTP

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Related structure data

Related structure data	1fxoS S: Starting model for refinement
Similar structure data	3pkp-6 1mp4-d 4b7x-5 5idt-1 3pkp-3 3pkp-5 3mx5-1 3gak-d 2z71-d 3mwp-3 Search similar-shape structures by Omokage search (details) 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: SSGCID-BuviA.00118.c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Glucose-1-phosphate thymidylyltransferase

B: Glucose-1-phosphate thymidylyltransferase

C: Glucose-1-phosphate thymidylyltransferase

D: Glucose-1-phosphate thymidylyltransferase

133 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Glucose-1-phosphate thymidylyltransferase

B: Glucose-1-phosphate thymidylyltransferase

defined by author&software
66.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Glucose-1-phosphate thymidylyltransferase

D: Glucose-1-phosphate thymidylyltransferase

defined by author&software
66.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.410, 115.580, 95.810
Angle α, β, γ (deg.)	90.000, 90.360, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-327- HOH

#1: Protein	Glucose-1-phosphate thymidylyltransferase Mass: 33318.730 Da / Num. of mol.: 4 / Fragment: BuviA.00118.c.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria) Strain: G4 / LMG 22486 / Gene: Bcep1808_3215 / Plasmid: BuviA.00118.c.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A4JIV2, glucose-1-phosphate thymidylyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Glucose-1-phosphate thymidylyltransferase

Mass: 33318.730 Da / Num. of mol.: 4 / Fragment: BuviA.00118.c.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_3215 / Plasmid: BuviA.00118.c.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4JIV2, glucose-1-phosphate thymidylyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.33 Å³/Da / Density % sol: 47.32 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: BuviA.00118.c.B1.PS02537 at 20.28 mg/ml, protein was mixed 1:1 with MCSG1(h5): 0.2 M potassium chloride, 20% (w/v) PEG-3350, cryoprotected with 20% ethylene glycol

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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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2016 / Details: Beryllium Lenses

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: 2.3→50 Å / Num. obs: 54334 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / B_iso Wilson estimate: 41.64 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.061 / Net I/σ(I): 15.09

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.3-2.36		0.552	2.36	1	100
2.36-2.42		0.485	2.63	1	99.9
2.42-2.49		0.377	3.37	1	99.9
2.49-2.57		0.298	4.3	1	99.9
2.57-2.66		0.237	5.43	1	100
2.66-2.75		0.201	6.38	1	100
2.75-2.85		0.155	8.2	1	99.9
2.85-2.97		0.123	10.28	1	99.9
2.97-3.1		0.096	12.93	1	99.9
3.1-3.25		0.075	16.11	1	100
3.25-3.43		0.059	20.23	1	100
3.43-3.64		0.05	24.28	1	100
3.64-3.89		0.044	27.14	1	100
3.89-4.2		0.038	31.61	1	100
4.2-4.6		0.037	33.57	1	100
4.6-5.14		0.034	35.13	1	100
5.14-5.94		0.034	34	1	100
5.94-7.27		0.035	33.97	1	99.9
7.27-10.29		0.032	40.1	1	100
	10.29	0.031	40.63	1	96.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1FXO

1fxo

Resolution: 2.3→48.611 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.61

	R_factor	Num. reflection	% reflection
R_free	0.2309	2088	3.84 %
R_work	0.1761	-	-
obs	0.1781	54309	99.87 %

Solvent computation

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

Displacement parameters

B_iso max: 141.84 Å² / B_iso mean: 56.0287 Å² / B_iso min: 26.34 Å²

Refinement step

Cycle: final / Resolution: 2.3→48.611 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8477	0	0	195	8672
B_iso mean	-	-	-	48.7	-
Num. residues	-	-	-	-	1152

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8702
X-RAY DIFFRACTION	f_angle_d	0.935	11902
X-RAY DIFFRACTION	f_chiral_restr	0.057	1337
X-RAY DIFFRACTION	f_plane_restr	0.006	1567
X-RAY DIFFRACTION	f_dihedral_angle_d	12.326	5116

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3001-2.3536	0.3153	143	0.2531	3454	3597	100
2.3536-2.4124	0.3053	146	0.2374	3472	3618	100
2.4124-2.4776	0.2977	154	0.2168	3432	3586	100
2.4776-2.5506	0.307	174	0.2125	3434	3608	100
2.5506-2.6329	0.2701	164	0.1963	3436	3600	100
2.6329-2.727	0.3147	129	0.2018	3502	3631	100
2.727-2.8361	0.2844	149	0.1991	3457	3606	100
2.8361-2.9652	0.2547	138	0.204	3478	3616	100
2.9652-3.1215	0.2563	117	0.197	3509	3626	100
3.1215-3.317	0.254	100	0.1956	3490	3590	100
3.317-3.5731	0.2715	135	0.1862	3504	3639	100
3.5731-3.9325	0.2092	138	0.1684	3473	3611	100
3.9325-4.5012	0.1795	124	0.1414	3530	3654	100
4.5012-5.6697	0.1813	137	0.1449	3515	3652	100
5.6697-48.622	0.187	140	0.1585	3535	3675	99

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	6.5889	-2.8612	1.1458	1.6706	-0.4315	2.3199	0.0999	0.3184	-0.2732	0.033	0.0754	0.099	0.0349	-0.1521	-0.2084	0.3202	-0.0683	0.084	0.3942	0.0321	0.3093	18.7412	3.3035	37.1709
2	1.5562	-0.4151	-0.2557	2.2747	0.0979	3.8971	0.068	-0.1762	0.2033	-0.0078	0.1801	-0.3592	-0.1813	0.2306	-0.2156	0.2577	-0.0633	0.0127	0.4442	-0.0819	0.4179	28.6453	2.0959	42.9756
3	5.9017	-3.8249	0.99	9.8697	-2.6338	5.0121	-0.0341	-1.502	0.3314	0.5704	0.3509	0.6521	0.8758	-0.8193	-0.3273	0.5432	-0.0404	-0.0313	0.7886	0.0108	0.4423	16.3574	-12.0288	55.2041
4	2.9538	-1.2803	-0.3586	2.7954	0.3895	1.9626	0.0199	-0.271	-0.1872	0.2788	0.1411	-0.0584	0.1552	-0.0214	-0.1447	0.2988	-0.0683	-0.0599	0.391	0.0024	0.2922	21.1771	-7.2878	49.302
5	6.3081	-0.125	-1.5794	3.711	0.2327	3.4387	0.2291	-0.394	0.7706	-0.0582	0.014	-0.4684	-0.706	-0.3607	-0.2182	0.624	-0.0551	0.069	0.462	-0.2138	0.5745	25.3948	21.7331	46.9305
6	0.8245	-1.2751	0.1887	2.7744	-1.5754	2.0561	-0.1361	1.0571	1.0765	-0.1688	-0.3432	-0.2374	-0.67	0.3367	0.2139	0.5141	0.0045	0.211	0.7151	0.1686	0.5203	6.4986	19.7743	23.588
7	1.5733	0.426	-0.129	1.3632	-0.6451	2.1787	0.1564	0.8393	0.2336	-0.4423	0.031	-0.2046	-0.0772	-0.1377	-0.0818	0.5483	0.1442	0.1538	0.7944	0.1275	0.4361	4.9449	14.3893	19.0542
8	2.1711	-0.0078	0.9218	4.3243	-3.2845	3.6821	0.0175	0.5091	1.0126	0.2203	0.0732	0.2319	-0.5007	-0.3909	0.0025	0.5287	0.1667	0.1051	0.7284	0.2642	0.6185	-9.6851	26.1635	25.3346
9	3.3861	-0.3936	0.4807	1.9302	-0.9551	5.6561	-0.177	0.4012	1.4345	-0.3227	0.3768	-0.1408	-0.4693	0.0289	-0.0023	0.7612	0.2167	0.1582	0.8653	0.4266	0.9108	-4.251	33.2883	17.0683
10	2.8764	0.8484	1.4746	2.637	0.7986	2.652	-0.1017	-0.0742	-0.0911	0.3057	0.1865	0.0921	-0.1172	-0.3818	-0.1037	0.3659	0.0898	0.0783	0.4571	0.0523	0.2939	-3.2872	14.1005	38.1192
11	2.4562	1.903	-0.2869	3.4155	-2.3411	6.8488	0.0114	0.2663	-0.3301	-0.5207	-0.0719	-0.1349	0.5746	-0.298	0.0287	0.467	0.0375	0.0446	0.5538	-0.0739	0.3898	-4.3871	-2.6193	24.7791
12	2.0552	1.1841	1.1135	1.0686	1.1206	2.4612	0.2464	-0.6399	-0.3653	-0.0441	0.035	0.2098	0.1121	-0.3081	-0.3793	0.4612	-0.1114	0.0952	0.3579	0.0151	0.5296	32.8615	1.2632	12.3023
13	9.6641	-5.5839	2.4129	7.4366	-2.6665	0.9812	-0.1158	-0.367	-0.2006	0.2648	0.1019	-0.0641	0.0576	-0.3567	-0.0449	0.3901	-0.0971	0.0753	0.3338	-0.0709	0.2925	44.5316	9.0559	15.1067
14	2.1142	0.0475	0.1709	2.391	-1.2095	2.7062	-0.0648	-0.0342	0.043	0.1187	0.1348	0.3519	-0.1554	-0.1673	-0.0316	0.3369	-0.0817	0.1071	0.3745	-0.0709	0.4605	29.7729	10.4096	13.5447
15	3.0294	3.2897	1.0399	6.3264	-1.3515	5.279	-0.1158	-0.1062	-0.5077	-0.1161	0.4354	-0.1648	0.5694	-0.1125	-0.3488	0.4618	-0.1004	0.1616	0.4899	-0.117	0.5598	25.9972	-1.2113	17.8931
16	3.2478	1.3708	-0.174	3.1906	-1.0471	2.5354	-0.2751	0.1754	-0.6735	-0.537	0.1373	-0.1341	0.8816	-0.2516	0.1026	0.6192	-0.1564	0.1088	0.4315	-0.1276	0.5671	30.3741	-6.7996	0.55
17	5.9052	-1.6252	3.6842	0.8723	-1.7875	7.4268	0.0803	0.1125	0.1048	-0.1593	0.0266	-0.3089	0.2459	-0.2106	-0.0309	0.377	-0.0899	0.1286	0.3105	-0.076	0.326	45.8035	8.2473	0.6434
18	2.3961	0.7043	-3.2617	3.9554	-1.6783	6.0996	-0.1555	0.4907	0.341	0.3535	0.1918	0.1614	-0.544	0.1117	-0.1001	0.3773	-0.0371	0.0135	0.3871	-0.0193	0.4848	29.6011	19.2521	1.8063
19	6.6051	-1.2878	-4.9408	5.0471	-1.8194	5.9334	0.5182	-0.5369	1.1295	0.7144	-0.242	0.191	-1.782	0.4542	-0.4185	0.7856	-0.1334	0.1222	0.4168	-0.024	0.7389	32.7586	27.7034	6.2705
20	7.0299	3.5576	4.2144	2.8367	3.0755	4.2342	-0.4368	-0.5098	0.2241	0.2262	0.0031	0.2717	-0.487	0.0662	0.467	0.487	-0.0422	0.0947	0.3531	-0.0179	0.4386	54.0689	22.4165	25.1783
21	3.9607	-4.8936	0.3789	6.0764	-0.7143	1.5614	-0.4562	-0.0922	-0.6469	0.0602	0.1995	0.402	-0.0145	-0.2047	0.1103	0.465	-0.1321	0.0801	0.3972	-0.0279	0.3662	49.1432	14.0872	17.6031
22	3.9627	0.4167	-0.8228	4.4481	0.8748	4.9555	0.1272	-0.6212	-0.4528	0.7163	-0.3352	0.1919	0.4165	-0.5071	0.3029	0.5421	-0.1415	0.0403	0.4976	0.0062	0.3599	56.0177	13.58	29.4764
23	4.2319	0.2129	-1.1534	4.1474	1.2538	4.5885	-0.0014	-0.2922	0.133	0.4149	-0.1697	-0.0489	-0.1648	0.0328	0.0681	0.3919	-0.085	-0.0551	0.3665	-0.001	0.2919	63.253	23.4444	28.5735
24	4.1534	0.426	-0.4182	5.563	0.7911	5.6232	0.0278	-0.0988	0.6189	-0.1887	-0.1669	-0.0308	-0.5678	0.2252	0.1609	0.3719	-0.1277	-0.0732	0.3541	-0.0312	0.491	64.7055	35.5004	22.4304
25	1.1353	0.4214	0.359	2.0292	0.8849	3.0662	-0.0851	-0.0396	-0.0756	0.098	-0.0021	-0.212	0.0708	0.2542	0.0641	0.3408	-0.0573	0.0279	0.3541	0.0084	0.3581	64.5058	18.5178	18.7538
26	7.9405	-6.917	-0.254	8.908	-2.6471	2.8764	0.0399	0.2893	-1.8962	0.9952	-0.5126	0.8941	1.0698	-0.5376	0.4025	0.7134	-0.0643	0.0328	0.3759	-0.0508	0.9261	61.7245	-3.829	21.9324

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 35 )	A	2 - 35
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 36 through 139 )	A	36 - 139
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 140 through 156 )	A	140 - 156
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 157 through 246 )	A	157 - 246
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 247 through 290 )	A	247 - 290
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 19 )	B	3 - 19
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 20 through 104 )	B	20 - 104
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 105 through 182 )	B	105 - 182
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 183 through 218 )	B	183 - 218
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 219 through 247 )	B	219 - 247
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 248 through 290 )	B	248 - 290
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 2 through 17 )	C	2 - 17
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 18 through 35 )	C	18 - 35
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 36 through 76 )	C	36 - 76
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 77 through 100 )	C	77 - 100
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 101 through 218 )	C	101 - 218
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 219 through 246 )	C	219 - 246
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 247 through 265 )	C	247 - 265
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 266 through 290 )	C	266 - 290
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 2 through 19 )	D	2 - 19
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 20 through 35 )	D	20 - 35
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 36 through 76 )	D	36 - 76
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 77 through 139 )	D	77 - 139
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 140 through 199 )	D	140 - 199
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 200 through 265 )	D	200 - 265
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 266 through 290 )	D	266 - 290

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