PDB-5ldp: Crystal structure of E.coli LigT complexed with ATP

ID or keywords:

Entry

Database: PDB / ID: 5ldp

Title

Crystal structure of E.coli LigT complexed with ATP

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 / ATP binding
Similarity search - Function

Biological species

Escherichia coli BL21 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 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 ...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_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ldp.cif.gz	172.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5ldp.ent.gz	136.9 KB	Display	PDB format
PDBx/mmJSON format	5ldp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5ldp_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5ldp_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5ldp_validation.xml.gz	20.4 KB	Display
Data in CIF	5ldp_validation.cif.gz	28.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ld/5ldp ftp://data.pdbj.org/pub/pdb/validation_reports/ld/5ldp	HTTPS FTP

-
Related structure data

Related structure data	5ldiSC 5ldjC 5ldkC 5ldmC 5ldoC 5ldqC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5ldk-1 5ldq-3 5ldq-4 5f4q-3 4qak-2 3sw8-d 5ldq-2 5x2j-d 5u7c-1 6i3c-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: RNA 2',3'-cyclic phosphodiesterase

B: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

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

1

A: RNA 2',3'-cyclic phosphodiesterase

hetero molecules

defined by author
20.7 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
21.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	102.150, 73.470, 77.610
Angle α, β, γ (deg.)	90.00, 128.34, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	RNA 2',3'-cyclic phosphodiesterase / RNA 2' / 3'-CPDase Mass: 20045.029 Da / Num. of mol.: 2 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-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.18 %
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

-
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: 1.8→30 Å / Num. obs: 41617 / % possible obs: 99.2 % / Redundancy: 3.38 % / B_iso Wilson estimate: 28.8 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.047 / Net I/σ(I): 15.47
Reflection shell	Resolution: 1.8→1.85 Å / Redundancy: 3.33 % / R_merge(I) obs: 1.061 / Mean I/σ(I) obs: 1.31 / CC_1/2: 0.508 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1467	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDBid: 5ldi

5ldi

Resolution: 1.8→19.703 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.98

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2085	1975	4.75 %	Random selection
R_work	0.1689	-	-	-
obs	0.1708	41615	99.73 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 42.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→19.703 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2749	0	100	308	3157

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	3097
X-RAY DIFFRACTION	f_angle_d	1.242	4254
X-RAY DIFFRACTION	f_dihedral_angle_d	16.958	1167
X-RAY DIFFRACTION	f_chiral_restr	0.052	447
X-RAY DIFFRACTION	f_plane_restr	0.005	546

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	0.336	147	0.2949	2810	X-RAY DIFFRACTION	100
1.845-1.8948	0.3155	137	0.2744	2798	X-RAY DIFFRACTION	100
1.8948-1.9505	0.2916	141	0.2322	2790	X-RAY DIFFRACTION	100
1.9505-2.0134	0.2603	146	0.2102	2838	X-RAY DIFFRACTION	100
2.0134-2.0853	0.2347	135	0.1949	2826	X-RAY DIFFRACTION	100
2.0853-2.1687	0.2589	141	0.183	2854	X-RAY DIFFRACTION	100
2.1687-2.2672	0.2118	147	0.1716	2787	X-RAY DIFFRACTION	100
2.2672-2.3866	0.2279	136	0.1781	2842	X-RAY DIFFRACTION	100
2.3866-2.5358	0.2221	140	0.1762	2846	X-RAY DIFFRACTION	100
2.5358-2.7311	0.2444	142	0.1803	2837	X-RAY DIFFRACTION	100
2.7311-3.0051	0.2195	140	0.17	2830	X-RAY DIFFRACTION	100
3.0051-3.438	0.1893	139	0.165	2845	X-RAY DIFFRACTION	100
3.438-4.3239	0.1695	138	0.1378	2872	X-RAY DIFFRACTION	100
4.3239-19.7037	0.1765	146	0.1492	2865	X-RAY DIFFRACTION	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	4.7267	-3.858	-0.621	6.8513	1.6372	3.5918	-0.0704	0.0047	0.0485	0.0346	0.1573	0.7001	0.3717	-0.9056	-0.0994	0.22	-0.0207	0.0024	0.3908	0.1239	0.2437	-24.2022	-0.5714	13.606
2	5.6617	-0.0434	1.8105	7.806	-3.8028	8.0833	0.1063	-0.5763	-0.822	-0.1342	0.1382	-0.0311	0.8487	0.046	-0.1362	0.3997	0.0397	-0.0452	0.2129	0.0782	0.3631	-6.6077	-11.5278	19.8678
3	6.7934	-1.7895	1.4306	2.8441	-1.2466	5.0959	0.1395	-0.3724	-0.2498	0.0229	0.2105	0.6876	-0.244	-0.9265	-0.3087	0.2512	0.059	0.0378	0.355	0.0481	0.3214	-26.5461	4.246	13.2304
4	3.4857	-0.6076	0.4686	0.8246	0.1714	0.6354	-0.2064	-0.6986	0.1096	0.2782	0.1211	0.0268	-0.0476	-0.2686	-0.0326	0.2714	0.0505	0.0107	0.2641	-0.0289	0.2271	-8.9513	4.2104	20.9123
5	6.1941	-3.7903	-2.8355	4.2031	0.7431	8.0805	0.0282	-0.7638	1.1374	0.3428	0.2339	0.198	-0.693	-0.2829	-0.1761	0.4709	0.1234	0.0303	0.2329	-0.0107	0.3275	-20.3068	13.8411	15.6979
6	6.4777	3.5884	3.9909	5.7194	1.1778	4.712	0.1408	-3.9466	2.3827	2.1123	0.4053	0.5624	0.8249	-1.8361	-0.3779	0.9107	0.1579	0.1265	1.0591	-0.1291	0.5561	-20.9957	10.0035	25.0304
7	0.1931	0.6488	-0.777	3.9452	-4.481	5.1596	0.0427	-1.5256	-0.6225	0.9098	0.4005	0.875	0.3045	0.0035	-0.3787	0.4759	0.0518	0.0748	0.6829	0.2184	0.3629	-13.3271	-6.1001	27.9298
8	4.6079	-0.8612	-0.9229	0.5227	0.6047	0.5368	0.0144	-0.7281	-0.1708	0.1003	0.0986	0.0029	0.4607	0.1818	-0.1031	0.2478	0.0355	-0.0078	0.2422	0.0165	0.2337	-2.4232	-2.1904	18.5656
9	4.7535	0.1137	-0.0809	6.7301	-1.27	6.5754	-0.1644	-0.7245	-1.3651	0.5406	-0.033	0.2883	0.9336	-0.536	0.1442	0.3818	-0.0231	0.0749	0.3971	0.1382	0.4726	-24.3511	-5.1089	13.9931
10	5.7418	0.5077	0.8893	7.0032	-1.0954	6.7832	-0.2758	0.0552	-0.3942	-0.0447	0.1372	0.101	0.2766	-0.3199	0.1147	0.1893	0.0518	0.0376	0.1152	0.0019	0.2072	-20.3814	1.3072	7.4776
11	3.8103	-0.5789	-0.5142	3.0077	1.959	6.73	-0.1994	-0.1861	-0.3482	0.1795	0.0297	-0.0628	0.57	-0.166	0.199	0.2156	0.0162	-0.02	0.1419	0.0214	0.2311	15.4901	-6.4941	12.4493
12	7.4241	-4.689	-5.5895	3.0151	3.7863	5.5809	-0.7497	-0.5506	-0.6646	0.5652	0.4554	0.0714	0.6621	0.4018	0.2665	0.2884	0.091	-0.001	0.2491	-0.0335	0.3119	22.1094	-8.9239	13.029
13	2.9884	1.1651	1.601	3.4666	-2.8231	7.0124	-0.5228	-1.454	0.3416	1.5628	0.1691	-0.3489	-0.3964	0.4095	0.2022	0.6002	0.0465	-0.1313	0.7207	-0.1552	0.3506	12.7011	6.4813	31.424
14	1.1222	-0.0331	-1.3078	2.362	1.3786	2.6693	0.0024	-0.2415	0.307	0.2584	0.1394	-0.3615	-0.1305	0.3665	-0.0948	0.2422	-0.0246	-0.0329	0.2014	-0.0406	0.2451	20.8918	4.3565	8.9002
15	3.3818	-0.4322	1.4657	4.8456	-0.2243	2.9907	0.581	-1.0709	1.344	0.8536	-0.1278	-0.3224	-1.5884	1.3577	0.1721	0.5135	-0.1482	-0.0021	0.4365	-0.1915	0.5456	15.6763	13.6961	20.1406
16	3.6363	-0.5484	-0.4724	2.0627	0.4591	3.8334	-0.0376	-0.2406	0.1976	0.1322	0.1679	-0.4308	0.1335	0.6446	-0.0646	0.2159	0.0245	-0.0382	0.2355	-0.0591	0.2668	22.4039	-1.7444	8.8066
17	4.1192	-0.5341	-0.568	2.9477	-0.6949	4.2884	-0.1876	-0.5831	-0.4214	0.264	0.0308	-0.2286	0.6152	0.3133	0.0741	0.3621	0.0781	-0.0415	0.2821	0.0117	0.3111	10.6162	-3.0484	22.5105

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 14 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 15 through 38 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 39 through 66 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 96 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 97 through 113 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 114 through 124 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 125 through 134 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 135 through 150 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 151 through 162 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 163 through 176 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 3 through 28 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 29 through 46 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 47 through 66 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 67 through 96 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 97 through 112 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 113 through 150 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 151 through 176 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi