PDB-5ldj: Crystal structure of E.coli LigT complexed with phosphate

ID or keywords:

Entry

Database: PDB / ID: 5ldj

Title

Crystal structure of E.coli LigT complexed with phosphate

Components

RNA 2',3'-cyclic phosphodiesterase

Keywords

HYDROLASE / Enzyme / 2H phosphoesterase/ligase

Function / homology

Function and homology information

RNA 2',3'-cyclic 3'-phosphodiesterase / RNA 2',3'-cyclic 3'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / ligase activity / ATP binding
Similarity search - Function

Biological species

Escherichia coli BL21 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.802 Å

Authors

Myllykoski, M. / Kursula, P.

Citation

Journal: PLoS ONE / Year: 2017
Title: Structural aspects of nucleotide ligand binding by a bacterial 2H phosphoesterase.
Authors: Myllykoski, M. / Kursula, P.

History

Deposition	Jun 27, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 18, 2017	Provider: repository / Type: Initial release
Revision 1.1	Feb 8, 2017	Group: Database references
Revision 1.2	Jan 17, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Jan 10, 2024	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	5ldj.cif.gz	285.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5ldj.ent.gz	237.1 KB	Display	PDB format
PDBx/mmJSON format	5ldj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5ldj_validation.pdf.gz	465.7 KB	Display	wwPDB validaton report
Full document	5ldj_full_validation.pdf.gz	470.9 KB	Display
Data in XML	5ldj_validation.xml.gz	24.6 KB	Display
Data in CIF	5ldj_validation.cif.gz	32.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldj ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldj	HTTPS FTP

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Related structure data

Related structure data	5ldiSC 5ldkC 5ldmC 5ldoC 5ldpC 5ldqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ldk-2 3r8j-1 1uei-1 5ldm-1 7nmm-3 3hi2-2 3uyw-3 7nmm-7 5ldo-2 7nmm-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5ldiSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA 2',3'-cyclic phosphodiesterase

B: RNA 2',3'-cyclic phosphodiesterase

C: RNA 2',3'-cyclic phosphodiesterase

D: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

1

A: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

2

B: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

3

C: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

4

D: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

Unit cell

Length a, b, c (Å)	54.730, 63.520, 67.370
Angle α, β, γ (deg.)	106.26, 106.14, 103.06
Int Tables number	1
Space group name H-M	P1

#1: Protein	RNA 2',3'-cyclic phosphodiesterase / RNA 2' / 3'-CPDase Mass: 20045.029 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli BL21(DE3) (bacteria) / Gene: thpR, ECBD_3472 / Plasmid: pTH 27 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A140NFI1, Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.54 Å³/Da / Density % sol: 51.64 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Tris-HCl pH 7.5, 0.2 M MgCl2, 18% (w/v) PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.04 Å / Relative weight: 1
Reflection	Resolution: 2.8→30 Å / Num. obs: 18651 / % possible obs: 95.7 % / Redundancy: 2.21 % / B_iso Wilson estimate: 42.6 Å² / CC_1/2: 0.978 / R_merge(I) obs: 0.126 / Net I/σ(I): 7.21
Reflection shell	Resolution: 2.8→2.88 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.942 / Mean I/σ(I) obs: 1.02 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBid:5LDI

5ldi

Resolution: 2.802→22.956 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.09

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	1859	9.97 %	Random selection
R_work	0.2177	-	-	-
obs	0.2218	18643	96.24 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 60.8 Å²

Refinement step

Cycle: LAST / Resolution: 2.802→22.956 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5412	0	25	21	5458

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5624
X-RAY DIFFRACTION	f_angle_d	0.705	7657
X-RAY DIFFRACTION	f_dihedral_angle_d	11.538	2078
X-RAY DIFFRACTION	f_chiral_restr	0.028	820
X-RAY DIFFRACTION	f_plane_restr	0.003	991

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 (%)
2.8023-2.878	0.4078	144	0.3436	1279	X-RAY DIFFRACTION	95
2.878-2.9625	0.379	133	0.3312	1290	X-RAY DIFFRACTION	96
2.9625-3.0579	0.3326	149	0.2981	1313	X-RAY DIFFRACTION	97
3.0579-3.1669	0.3119	151	0.2812	1285	X-RAY DIFFRACTION	97
3.1669-3.2934	0.3198	142	0.2681	1292	X-RAY DIFFRACTION	98
3.2934-3.4428	0.31	138	0.2675	1329	X-RAY DIFFRACTION	98
3.4428-3.6236	0.2744	149	0.2243	1292	X-RAY DIFFRACTION	97
3.6236-3.8497	0.3083	136	0.2492	1235	X-RAY DIFFRACTION	92
3.8497-4.1453	0.247	142	0.1879	1309	X-RAY DIFFRACTION	97
4.1453-4.5595	0.2081	147	0.1636	1298	X-RAY DIFFRACTION	96
4.5595-5.2125	0.1878	148	0.1526	1291	X-RAY DIFFRACTION	97
5.2125-6.542	0.2146	139	0.1876	1316	X-RAY DIFFRACTION	98
6.542-22.9567	0.1774	141	0.1624	1255	X-RAY DIFFRACTION	93

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	3.4121	-0.969	0.7687	4.6424	-1.3329	1.2992	0.2055	0.0075	-0.0159	-0.2989	0.0344	0.5622	0.089	-0.1915	-0.1663	0.287	-0.0342	0.0092	0.2949	0.0034	0.2887	-3.7849	91.7477	-6.5588
2	5.483	-0.403	1.8873	4.0662	1.5861	3.3308	-0.1472	0.1115	-0.6253	0.2631	0.5101	0.45	0.3444	-0.4397	-0.3557	0.45	-0.1121	-0.0414	0.3841	0.1438	0.4438	1.7825	85.0312	-0.2321
3	5.7432	-0.0467	0.6923	3.9975	-1.2729	5.1501	-0.19	0.3604	-0.2131	-0.894	0.2112	0.5629	0.1774	-0.0882	-0.1459	0.3783	-0.0276	-0.0669	0.2142	0.0115	0.5046	-3.3695	95.769	-14.6448
4	3.2562	0.5707	1.6044	6.758	-0.7014	3.7296	-0.2353	0.2253	-0.4008	-1.3462	0.353	-0.8205	0.2959	0.7693	-0.2213	0.4123	0.0847	0.0949	0.4621	-0.0139	0.3437	6.4995	114.5273	-26.9356
5	1.3654	-0.6605	1.1884	3.2901	-0.4888	3.5799	-0.1367	-0.0263	0.1644	-0.2093	0.0864	0.2222	-0.4068	-0.203	0.0103	0.2601	0.0039	-0.0883	0.3733	-0.0149	0.4336	-1.434	124.9072	-19.6285
6	2.2303	1.8182	0.4003	3.7595	-0.7456	5.6651	-0.227	0.3786	0.2401	-1.1326	0.2108	1.0636	-0.1363	-0.19	-0.1382	0.5397	0.0944	-0.1838	0.2953	0.0181	0.474	0.4336	118.1049	-24.9157
7	7.2418	-0.0897	-1.5614	8.107	2.5918	7.3844	-0.1222	0.3918	0.5911	-0.6426	-0.1998	-0.4785	-0.6667	0.1276	0.1121	0.3472	-0.0066	-0.1234	0.1934	0.0969	0.3948	10.3599	126.2179	-19.5762
8	4.5092	1.8082	-0.724	4.8259	-1.0684	2.5072	0.2487	-0.8604	-1.4526	0.2371	0.0632	-0.5531	0.3404	0.1906	0.3742	0.8693	-0.1118	-0.4624	0.2711	0.235	0.3687	-18.7054	113.3215	-44.336
9	6.8888	3.0641	-1.5368	6.15	0.9724	2.9125	-0.0394	0.1033	-0.8229	-0.0765	-0.1639	-0.774	-0.0555	0.5592	-0.0055	0.2991	0.0787	0.0564	0.4088	0.0568	0.3852	-2.9753	126.091	-53.5987
10	3.6683	1.553	-0.0721	3.0956	-0.1948	1.6439	0.5093	-0.5037	-0.3848	0.6101	-0.5189	-0.0376	0.2578	-0.0482	0.0172	0.549	-0.0214	-0.1001	0.3968	0.0121	0.2829	-21.4634	120.3406	-42.9502
11	2.5475	1.9077	-0.6989	1.943	-0.4683	1.6797	0.1237	-1.1621	-0.2416	0.4005	-0.3455	-0.5165	-0.0763	0.3205	0.0734	0.7255	-0.1142	-0.0225	0.3685	0.0362	0.4149	-9.5287	131.2335	-40.8678
12	4.7672	2.6071	1.2061	3.4704	-1.7021	3.0233	-0.7728	-0.8173	-0.116	1.5011	-0.2771	0.8863	0.3723	-1.1484	0.0378	0.7643	-0.03	0.2202	0.7292	-0.0371	0.329	-26.2703	125.219	-37.472
13	2.6048	0.8166	-1.4188	4.9802	-0.5919	2.8279	-0.4034	-1.1422	0.2066	0.8029	-0.4489	-0.0275	0.9268	0.4977	0.2961	0.4212	-0.0645	-0.0799	0.5244	-0.1033	0.34	-12.8312	124.9337	-40.5329
14	3.1206	2.0697	-0.2211	6.9465	-1.3058	3.2044	-0.3183	-0.2372	-0.0123	0.5855	-0.5195	-1.1002	0.2788	0.8407	0.217	0.5995	0.0115	-0.0385	0.6192	0.0711	0.3791	-2.8769	132.6916	-47.9569
15	3.6337	1.4928	0.8805	4.8981	-0.0643	3.6004	0.3797	0.1535	-0.4622	-0.6911	-0.2413	-0.0998	0.5923	0.287	-0.0402	0.4394	-0.0284	0.0071	0.3101	0.0851	0.2766	-17.5697	116.9808	-49.1553
16	8.0085	0.5895	0.4324	6.3276	-0.0026	4.0196	0.1518	-0.0235	-0.6447	0.0125	-0.0708	-0.0742	0.6568	0.2429	-0.0974	0.4491	-0.0437	-0.0527	0.2312	0.0226	0.2818	-21.7794	115.6491	-49.8141
17	4.1079	1.7469	1.5063	3.5831	0.4647	7.1826	0.811	-0.1809	-0.4355	0.7155	-0.5456	-0.0651	0.0215	1.7752	0.2044	0.6365	-0.1669	-0.2449	0.315	-0.0555	0.5333	-22.0943	126.0275	6.7946
18	4.4642	0.0895	1.3304	4.1103	-1.2808	7.2403	-0.2139	0.6469	-0.302	-0.4093	0.1652	-0.1515	0.685	0.8138	0.0719	0.3317	0.017	0.0189	0.3175	-0.1265	0.3835	-26.4994	123.9353	-15.2978
19	1.999	0.6771	1.0802	1.895	-0.9252	7.6788	0.2183	0.0183	0.2091	0.8274	-0.137	-0.356	-0.3012	1.1324	0.0755	0.5879	-0.089	-0.1756	0.2689	-0.0025	0.7014	-23.566	128.5353	3.4096
20	2.2222	1.7309	-1.5728	3.7485	-0.2741	3.3987	0.0758	-1.4202	0.119	1.4356	-0.784	-0.7698	-0.4922	-0.2878	0.1242	1.0055	-0.1151	-0.2103	0.6414	-0.0359	0.5848	-23.8487	127.4143	19.2345
21	1.8035	0.4868	0.0516	2.7053	-1.2068	4.3076	-0.0695	-0.1096	0.4711	0.8421	-0.0323	0.1821	-0.7107	-0.4135	-0.3026	0.4842	0.0262	-0.013	0.1651	-0.0138	0.3392	-37.4584	127.666	1.3462
22	0.7364	0.17	0.8262	1.2649	-0.3086	3.3673	-0.2	0.4979	0.9531	-0.0031	0.1563	0.6348	-0.5474	-0.2415	-0.0337	0.3559	-0.0162	-0.0881	0.2767	0.0191	0.6184	-33.2403	135.2284	-7.7481
23	3.3487	-1.0971	-1.514	5.174	1.5485	8.463	-0.6458	0.0677	0.9664	0.8968	-0.0249	-0.1844	-0.9677	-0.0716	-0.5606	0.7296	-0.1152	0.0529	0.3675	0.0548	0.6731	-36.5976	132.1995	9.767
24	2.8461	-1.2319	-1.223	1.8974	-0.2217	6.5519	0.4713	-0.0877	0.8716	0.2261	0.2384	-0.3	-0.9845	0.1408	-0.8703	0.5345	-0.0227	-0.0887	0.3498	0.0021	0.5581	-29.0359	132.987	-3.8952
25	2.6658	-0.5625	2.9917	3.406	-0.7187	5.3976	-0.3256	0.7139	0.2679	-0.0905	0.3671	-0.226	-0.2794	0.5915	0.2423	0.3854	-0.0854	-0.085	0.3356	-0.0089	0.5122	-31.947	130.5812	-16.3936
26	2.6621	-0.0354	3.0274	3.5242	-0.4915	3.4839	0.1042	0.1333	-0.4896	0.152	-0.4989	-0.7212	-0.2886	0.168	0.0332	0.3808	-0.0273	0.0122	0.3074	-0.0395	0.2983	-24.8964	122.5373	2.5841
27	7.0273	0.1129	0.4641	4.4541	-1.8054	6.9823	0.1558	0.3317	-0.3533	0.4801	-0.0165	-0.5053	0.0045	-0.0038	0.1457	0.6574	-0.134	-0.1234	0.2134	0.0237	0.2868	-25.8636	120.4402	6.4279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 110 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 111 through 145 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 146 through 176 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 38 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 39 through 113 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 114 through 162 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 163 through 176 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 2 through 14 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 15 through 38 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 39 through 82 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 83 through 96 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 97 through 111 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 112 through 130 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 131 through 145 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 146 through 162 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 163 through 176 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 2 through 14 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 15 through 38 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 39 through 53 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 54 through 64 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 65 through 82 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 83 through 96 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 97 through 110 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 111 through 130 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 131 through 145 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 146 through 162 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 163 through 176 )

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