PDB-4pc3: Elongation factor Tu:Ts complex with partially bound GDP

ID or keywords:

Entry

Database: PDB / ID: 4pc3

Title

Elongation factor Tu:Ts complex with partially bound GDP

Components

Elongation factor Ts
Elongation factor Tu 1

Keywords

TRANSLATION / G:GEF:GDP complex / Elongation factor / Protein synthesis

Function / homology

Function and homology information

guanyl-nucleotide exchange factor complex / translational elongation / guanosine tetraphosphate binding / translation elongation factor activity / guanyl-nucleotide exchange factor activity / response to antibiotic / GTPase activity / GTP binding / RNA binding / zinc ion binding ...
Similarity search - Function

GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation domain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / : ...
Similarity search - Domain/homology

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8313 Å

Authors

Thirup, S.S.

Citation

Journal: J.Struct.Biol. / Year: 2015
Title: Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.
Authors: Thirup, S.S. / Van, L.B. / Nielsen, T.K. / Knudsen, C.R.

History

Deposition	Apr 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 6, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 1, 2015	Group: Database references
Revision 1.2	Jul 15, 2015	Group: Database references
Revision 1.3	Mar 7, 2018	Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	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	4pc3.cif.gz	761.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4pc3.ent.gz	646.7 KB	Display	PDB format
PDBx/mmJSON format	4pc3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pc3_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4pc3_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4pc3_validation.xml.gz	57.2 KB	Display
Data in CIF	4pc3_validation.cif.gz	86.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pc/4pc3 ftp://data.pdbj.org/pub/pdb/validation_reports/pc/4pc3	HTTPS FTP

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Related structure data

Related structure data	4pc1SC 4pc2C 4pc6C 4pc7C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pc6-2 4pc1-1 4pc2-2 4pc6-1 4pc1-2 4pc2-1 1xmx-2 1iye-d 2ej3-d 1iyd-d 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#81 - Sep 2006 Elongation Factors similarity (23) #121 - Jan 2010 70S Ribosomes similarity (13) #157 - Jan 2013 Transfer-Messenger RNA similarity (13) #104 - Aug 2008 Selenocysteine Synthase similarity (6) #245 - May 2020 Spliceosomes similarity (5) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

A: Elongation factor Tu 1

C: Elongation factor Ts

B: Elongation factor Tu 1

D: Elongation factor Ts

hetero molecules

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

1

A: Elongation factor Tu 1

C: Elongation factor Ts

hetero molecules

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

2

B: Elongation factor Tu 1

D: Elongation factor Ts

hetero molecules

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

Unit cell

Length a, b, c (Å)	74.000, 108.920, 194.770
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Elongation factor Tu 1 / EF-Tu 1 / P-43 Mass: 43340.465 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufA, b3339, JW3301 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47
#2: Protein	Elongation factor Ts / EF-Ts Mass: 30332.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsf, b0170, JW0165 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6P1
#3: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1158 / 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: 2.66 Å³/Da / Density % sol: 53.74 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM MES, 15% PEG 6000, 2.5% glucose, 76mM NH4 CH3COO, 100mM NH4-citrate, 5mM MgCl2, 1mM GDP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.033 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2003
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.83→58.92 Å / Num. obs: 136637 / % possible obs: 98.5 % / Redundancy: 6.5 % / R_merge(I) obs: 0.052 / Net I/σ(I): 16.3
Reflection shell	Resolution: 1.83→1.95 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.369 / Mean I/σ(I) obs: 3.9 / % possible all: 98.2

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Processing

Software

Name: PHENIX / Version: (phenix.refine: dev_1702) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4PC1

4pc1

Resolution: 1.8313→58.92 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 19.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1985	6098	4.51 %	random
R_work	0.1593	-	-	-
obs	0.1611	135282	97.39 %	-

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.8313→58.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9859	0	86	1158	11103

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	10301
X-RAY DIFFRACTION	f_angle_d	1.276	13930
X-RAY DIFFRACTION	f_dihedral_angle_d	13.877	3893
X-RAY DIFFRACTION	f_chiral_restr	0.054	1591
X-RAY DIFFRACTION	f_plane_restr	0.007	1807

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 (%)
1.8313-1.8522	0.3057	178	0.2704	3569	X-RAY DIFFRACTION	81
1.8522-1.874	0.3135	179	0.2547	4274	X-RAY DIFFRACTION	97
1.874-1.8968	0.2749	181	0.2327	4279	X-RAY DIFFRACTION	97
1.8968-1.9208	0.2606	175	0.2182	4213	X-RAY DIFFRACTION	97
1.9208-1.9461	0.2411	182	0.2075	4311	X-RAY DIFFRACTION	97
1.9461-1.9728	0.2267	179	0.207	4241	X-RAY DIFFRACTION	97
1.9728-2.0009	0.2558	180	0.2035	4284	X-RAY DIFFRACTION	97
2.0009-2.0308	0.2179	173	0.2065	4240	X-RAY DIFFRACTION	97
2.0308-2.0625	0.2141	179	0.1911	4271	X-RAY DIFFRACTION	97
2.0625-2.0964	0.2284	177	0.184	4253	X-RAY DIFFRACTION	96
2.0964-2.1325	0.2089	174	0.179	4227	X-RAY DIFFRACTION	96
2.1325-2.1713	0.2057	180	0.1806	4251	X-RAY DIFFRACTION	96
2.1713-2.2131	0.1946	171	0.1708	4245	X-RAY DIFFRACTION	96
2.2131-2.2582	0.2253	188	0.1611	4206	X-RAY DIFFRACTION	96
2.2582-2.3073	0.185	195	0.1632	4232	X-RAY DIFFRACTION	96
2.3073-2.361	0.2003	174	0.169	4193	X-RAY DIFFRACTION	95
2.361-2.42	0.2119	213	0.1696	4196	X-RAY DIFFRACTION	96
2.42-2.4855	0.2079	235	0.17	4382	X-RAY DIFFRACTION	100
2.4855-2.5586	0.2108	278	0.1607	4342	X-RAY DIFFRACTION	100
2.5586-2.6412	0.2012	273	0.1601	4366	X-RAY DIFFRACTION	100
2.6412-2.7356	0.2151	243	0.162	4385	X-RAY DIFFRACTION	100
2.7356-2.8451	0.2056	272	0.1613	4351	X-RAY DIFFRACTION	100
2.8451-2.9746	0.2237	242	0.1677	4407	X-RAY DIFFRACTION	100
2.9746-3.1314	0.2113	210	0.1647	4410	X-RAY DIFFRACTION	100
3.1314-3.3276	0.1879	303	0.1539	4337	X-RAY DIFFRACTION	100
3.3276-3.5845	0.2	274	0.1463	4418	X-RAY DIFFRACTION	100
3.5845-3.9452	0.1889	205	0.1429	4494	X-RAY DIFFRACTION	100
3.9452-4.5159	0.1521	177	0.1245	4536	X-RAY DIFFRACTION	100
4.5159-5.6888	0.1574	151	0.1287	4617	X-RAY DIFFRACTION	100
5.6888-58.9502	0.1723	157	0.1609	4654	X-RAY DIFFRACTION	97

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	4.6776	5.3601	4.7611	7.9781	5.5881	4.898	-0.1565	0.4885	0.123	-0.4654	0.8201	-0.61	-0.1352	1.3836	-0.6082	0.4358	0.0502	0.0148	0.6371	-0.0717	0.4415	18.5579	58.0748	71.5489
2	6.6721	4.8421	4.3696	5.0803	3.1361	5.1279	-0.1646	0.7684	0.2274	-0.3937	0.5316	-0.7753	-0.7418	0.6409	-0.2861	0.6009	-0.2667	0.0288	0.521	-0.0954	0.5865	23.7294	68.4113	71.0199
3	3.4673	0.7686	0.5061	5.3006	1.6913	3.5848	-0.2127	-0.0486	0.3588	0.0343	0.3102	-0.0398	-0.3939	0.0227	-0.0934	0.4216	0.0148	-0.0145	0.3777	-0.0027	0.3284	12.7427	60.1134	73.4761
4	6.2684	-2.3749	2.8388	6.8352	-3.8709	3.2032	-0.4063	-0.3794	0.632	0.613	0.17	-0.9616	-0.5364	0.104	0.3042	0.3848	0.1178	-0.0678	0.5496	-0.1712	0.3792	33.3224	45.3814	101.5942
5	1.1266	0.0619	-0.2919	1.5549	1.2292	2.8062	-0.0731	-0.3529	0.1654	0.0401	-0.0346	0.0093	-0.12	-0.0634	0.1485	0.189	0.0746	-0.0303	0.3275	-0.1094	0.2516	27.0872	35.5103	93.2231
6	5.087	-2.5359	3.9446	7.2734	-1.8557	5.4551	-0.3374	-0.8358	-0.0563	0.4035	0.6306	0.2442	-0.6695	-1.5828	-0.2499	0.4799	0.1618	-0.0322	0.7445	0.1736	0.4245	-7.0573	61.9533	57.4995
7	9.8562	-7.7895	-1.5068	9.1246	0.6394	1.234	0.1512	-0.1539	-0.7023	-0.5942	0.1435	0.7482	0.0542	-0.54	-0.2861	0.4335	-0.0107	-0.0659	0.4206	0.1668	0.3711	-0.9364	55.5042	48.8984
8	2.1983	1.2718	0.3093	6.3193	0.4711	1.6929	-0.1057	0.1403	0.1196	0.2303	0.1081	0.1499	-0.1487	-0.016	-0.0094	0.1365	-0.0112	-0.0114	0.1494	0.0485	0.1678	7.135	34.899	56.1218
9	1.776	-1.1054	0.7141	6.3744	-1.3135	2.2414	-0.0918	0.1	0.0471	-0.028	0.1645	0.1611	-0.1659	-0.1427	-0.0664	0.1013	-0.046	0.0293	0.2127	0.0188	0.1746	8.0849	32.4452	54.2187
10	8.1147	-0.0444	-2.2828	0.8699	0.2542	2.1631	0.0237	0.3663	-0.3245	-0.1637	-0.0905	-0.0583	0.0783	-0.0124	0.058	0.2703	0.0282	-0.0351	0.1484	-0.0061	0.2183	30.821	16.9833	54.2901
11	9.2603	-3.9202	0.055	5.4947	-1.3862	1.4295	0.2378	0.6377	-0.0243	-0.3812	-0.1215	-0.092	0.2795	0.0321	-0.0391	0.3742	0.0071	-0.0235	0.354	-0.0716	0.2613	42.4093	12.2897	53.434
12	2.7781	0.5777	0.3179	1.3432	0.4717	2.5968	0.0872	-0.1077	-0.4784	0.0103	-0.0325	0.0499	0.5058	0.0373	-0.0243	0.1843	-0.0257	-0.0429	0.1338	-0.0205	0.2386	20.5483	12.8984	62.0652
13	3.5256	3.8363	2.1882	4.1446	2.4185	1.4395	-0.0631	-0.1061	0.2953	-0.5206	0.5988	-0.86	-0.6165	0.6198	-0.3807	0.5831	-0.1944	0.2224	0.4558	-0.1392	0.6018	26.2655	51.7241	60.5517
14	7.1241	0.8285	-1.5311	0.5667	-1.3444	3.2342	0.2656	-1.086	-0.604	1.5654	-0.0664	1.9065	0.5912	-1.9904	-0.2789	0.7092	-0.1807	0.2454	0.8104	0.1478	0.7678	30.7895	-17.4876	87.7901
15	9.4238	1.867	-2.0088	2.9081	-1.242	2.0619	0.2077	0.4271	0.4487	-0.6453	0.2669	-0.0322	0.1189	-0.1633	-0.4801	0.5413	-0.0722	-0.0054	0.4099	0.0367	0.4589	49.0271	-12.6176	74.5478
16	8.0906	5.4913	-5.187	4.1753	-4.9399	8.1956	0.0042	0.3925	-0.4501	-0.3289	-0.026	0.0375	0.8335	-0.1004	0.1353	0.6684	-0.191	-0.0557	0.4462	-0.0435	0.5783	39.7168	-23.5231	74.0771
17	3.9834	1.37	-0.824	4.4686	-0.7325	2.3871	0.0199	-0.2912	-0.57	0.1876	-0.0624	-0.0447	0.4752	0.033	0.0384	0.5452	-0.091	0.0136	0.3679	0.0205	0.4318	49.064	-15.5749	80.3557
18	2.9237	0.6836	0.0998	3.0115	-0.2028	1.5143	0.2839	-1.0737	-0.21	0.6701	-0.2646	0.2756	0.0513	-0.2306	-0.0182	0.2819	-0.1139	0.0323	0.5776	0.0413	0.1989	29.5936	7.5268	95.2438
19	5.5092	-3.3488	0.1612	7.2676	0.0707	3.639	-0.4997	-0.4035	-1.5638	0.2296	0.0936	-0.2141	1.335	1.2327	0.1659	0.6877	0.2706	0.0832	0.6161	0.0269	0.9234	73.5114	-21.3146	71.6214
20	8.329	-2.3789	4.9757	5.3486	-4.2434	6.6685	0.2002	-0.1607	-0.3734	-0.2591	-0.1085	-0.7771	0.6431	0.4721	-0.1034	0.3855	0.0375	0.0458	0.3489	-0.1377	0.4859	72.0752	-13.6937	62.2782
21	2.8652	1.5438	-0.2486	4.2439	-0.5424	1.2979	-0.0527	0.0034	0.099	0.1891	0.043	0.0896	-0.0053	0.1016	0.0075	0.2011	-0.0213	0.0267	0.1672	-0.058	0.1543	63.1274	8.4639	66.854
22	1.9217	-1.2824	-0.3707	5.2097	1.1135	1.3241	-0.1133	0.0036	0.088	-0.09	0.1709	-0.304	0.03	0.1308	-0.0369	0.1609	-0.0562	0.0021	0.1782	-0.0376	0.1449	62.885	11.0207	64.5477
23	5.0872	0.4584	2.2202	1.1025	-0.2582	3.5131	-0.1632	0.3704	0.6119	-0.0728	-0.0777	-0.0153	-0.2508	0.1016	0.1878	0.2476	0.0234	0.0275	0.1044	-0.0023	0.2577	43.1749	26.8671	57.0031
24	9.431	0.4896	5.5133	4.9193	1.7018	4.2575	0.193	0.0493	0.4964	-0.4258	-0.0616	0.0134	0.0277	-0.0289	-0.0833	0.3616	0.0123	0.0498	0.3823	0.0891	0.3659	30.3239	31.321	51.0062
25	0.8256	0.6759	-0.2923	2.0684	0.5644	2.3545	0.1058	0.0682	0.6463	0.0228	-0.1097	-0.1588	-0.5046	-0.2136	0.0501	0.2614	-0.0042	-0.0121	0.1144	-0.0395	0.3556	49.1841	30.6197	67.3065
26	5.8798	5.1461	-1.232	4.454	-1.1079	0.2462	-0.1524	-0.0842	-0.3388	-0.5774	0.4409	0.3474	0.7204	-1.0408	-0.0089	0.744	-0.3572	-0.1642	0.5678	0.1172	0.4745	42.2652	-6.7539	63.9549

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 65 through 198 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 199 through 230 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 231 through 393 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 2 through 32 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 33 through 51 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 52 through 106 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 107 through 161 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 162 through 207 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 208 through 225 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 226 through 259 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 260 through 280 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 8 through 12 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 13 through 23 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 24 through 41 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 56 through 198 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 199 through 393 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 2 through 32 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 33 through 51 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 52 through 106 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 107 through 161 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 162 through 204 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 205 through 225 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 226 through 259 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 260 through 280 )

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