PDB-5o96: Structure of the putative methyltransferase Lpg2936 from Legionel...

ID or keywords:

Entry

Database: PDB / ID: 5o96

Title

Structure of the putative methyltransferase Lpg2936 from Legionella pneumophila in complex with the bound cofactor SAM

Components

Ribosomal RNA small subunit methyltransferase E

Keywords

TRANSFERASE / RNA methyltransferase / RsmE-like / SAM /

S-adenosylmethionine

Function / homology

Function and homology information

16S rRNA (uracil1498-N3)-methyltransferase /

methyltransferase activity / rRNA processing /

methylation /

cytoplasm
Similarity search - Function

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Pinotsis, N. / Waksman, G.

Funding support

United Kingdom, 1items

Citation

Journal: Protein Sci. / Year: 2017
Title: Crystal structure of the Legionella pneumophila Lpg2936 in complex with the cofactor S-adenosyl-L-methionine reveals novel insights into the mechanism of RsmE family methyltransferases.
Authors: Pinotsis, N. / Waksman, G.

History

Deposition	Jun 15, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Jan 17, 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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PDBx/mmCIF format	5o96.cif.gz	785.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5o96.ent.gz	657.1 KB	Display	PDB format
PDBx/mmJSON format	5o96.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o9/5o96 ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o96	HTTPS FTP

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Related structure data

Related structure data	5o95SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o95-1 5o95-2 5nzh-1 5vm8-d 1vhy-d 5o4p-2 3o66-d 3kou-d 1z6t-1 4e8b-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

5o95SC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#116 - Aug 2009 Sulfotransferases similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Ribosomal RNA small subunit methyltransferase E

B: Ribosomal RNA small subunit methyltransferase E

C: Ribosomal RNA small subunit methyltransferase E

D: Ribosomal RNA small subunit methyltransferase E

E: Ribosomal RNA small subunit methyltransferase E

F: Ribosomal RNA small subunit methyltransferase E

G: Ribosomal RNA small subunit methyltransferase E

H: Ribosomal RNA small subunit methyltransferase E

hetero molecules

222 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribosomal RNA small subunit methyltransferase E

B: Ribosomal RNA small subunit methyltransferase E

hetero molecules

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

2

C: Ribosomal RNA small subunit methyltransferase E

D: Ribosomal RNA small subunit methyltransferase E

hetero molecules

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

3

E: Ribosomal RNA small subunit methyltransferase E

F: Ribosomal RNA small subunit methyltransferase E

hetero molecules

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

4

G: Ribosomal RNA small subunit methyltransferase E

H: Ribosomal RNA small subunit methyltransferase E

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.482, 98.740, 225.783
Angle α, β, γ (deg.)	90.00, 91.76, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	G-15- GLN

#1: Protein	Ribosomal RNA small subunit methyltransferase E / Mass: 27344.740 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lpg2936 / Production host: Escherichia coli (E. coli) References: UniProt: Q5ZRE6, 16S rRNA (uracil1498-N3)-methyltransferase
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine Mass: 398.437 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 585 / 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: 2.65 Å³/Da / Density % sol: 53.62 % / Description: nice cute tiny crystals
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Based on the C1 condition of the Morpheus screen 10% w/v PEG 20 000 20% v/v PEG MME 550, 0.03 M of each NPS 0.1 M MES/imidazole pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.99999 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 2.3→49.4 Å / Num. obs: 101902 / % possible obs: 97 % / Redundancy: 3.9 % / CC_1/2: 0.983 / R_merge(I) obs: 0.174 / Net I/σ(I): 4.3
Reflection shell	Resolution: 2.3→2.36 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 5031 / CC_1/2: 0.935 / % possible all: 97.2

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5O95

5o95

Resolution: 2.3→49.37 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7

	R_factor	Num. reflection	% reflection
R_free	0.2361	5119	5.04 %
R_work	0.1821	-	-
obs	0.1849	101584	99.63 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→49.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15221	0	216	585	16022

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	15831
X-RAY DIFFRACTION	f_angle_d	1.005	21402
X-RAY DIFFRACTION	f_dihedral_angle_d	17.165	9794
X-RAY DIFFRACTION	f_chiral_restr	0.055	2418
X-RAY DIFFRACTION	f_plane_restr	0.006	2770

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 (%)
2.3-2.3261	0.3356	163	0.2843	3245	X-RAY DIFFRACTION	99
2.3261-2.3535	0.3434	163	0.2738	3176	X-RAY DIFFRACTION	100
2.3535-2.3822	0.3383	175	0.2649	3179	X-RAY DIFFRACTION	99
2.3822-2.4124	0.2805	175	0.2568	3191	X-RAY DIFFRACTION	99
2.4124-2.4441	0.3159	164	0.2514	3169	X-RAY DIFFRACTION	99
2.4441-2.4776	0.2988	142	0.2505	3241	X-RAY DIFFRACTION	99
2.4776-2.513	0.2809	163	0.2432	3165	X-RAY DIFFRACTION	99
2.513-2.5505	0.3415	191	0.2413	3197	X-RAY DIFFRACTION	99
2.5505-2.5903	0.291	185	0.2296	3165	X-RAY DIFFRACTION	99
2.5903-2.6328	0.2964	214	0.2254	3116	X-RAY DIFFRACTION	99
2.6328-2.6782	0.2807	190	0.2202	3195	X-RAY DIFFRACTION	99
2.6782-2.7269	0.2803	158	0.2126	3190	X-RAY DIFFRACTION	100
2.7269-2.7793	0.275	170	0.2172	3212	X-RAY DIFFRACTION	99
2.7793-2.8361	0.2968	136	0.2119	3239	X-RAY DIFFRACTION	100
2.8361-2.8977	0.2645	141	0.2077	3259	X-RAY DIFFRACTION	100
2.8977-2.9651	0.2964	151	0.2154	3202	X-RAY DIFFRACTION	100
2.9651-3.0393	0.292	164	0.2098	3215	X-RAY DIFFRACTION	100
3.0393-3.1214	0.246	150	0.2055	3255	X-RAY DIFFRACTION	100
3.1214-3.2133	0.2667	166	0.2051	3227	X-RAY DIFFRACTION	100
3.2133-3.317	0.279	176	0.201	3219	X-RAY DIFFRACTION	100
3.317-3.4355	0.2474	162	0.1981	3219	X-RAY DIFFRACTION	100
3.4355-3.573	0.2655	210	0.1901	3184	X-RAY DIFFRACTION	100
3.573-3.7356	0.2053	191	0.1731	3202	X-RAY DIFFRACTION	100
3.7356-3.9324	0.224	156	0.155	3235	X-RAY DIFFRACTION	100
3.9324-4.1787	0.1932	166	0.1376	3248	X-RAY DIFFRACTION	100
4.1787-4.5011	0.1861	214	0.1286	3215	X-RAY DIFFRACTION	100
4.5011-4.9537	0.1576	175	0.1216	3239	X-RAY DIFFRACTION	100
4.9537-5.6696	0.2075	161	0.1468	3241	X-RAY DIFFRACTION	100
5.6696-7.1397	0.1945	178	0.1641	3280	X-RAY DIFFRACTION	100
7.1397-49.3814	0.1812	169	0.1498	3345	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	1.7614	0.0161	-0.6067	1.9376	0.0068	1.9167	0.1594	-0.4902	-0.0767	0.6491	-0.0927	0.1851	0.0207	-0.0746	-0.0872	0.4131	-0.0701	-0.0208	0.348	0.0428	0.1887	19.6124	-7.3642	92.5985
2	1.1221	0.2453	-0.2005	0.7864	0.0566	1.8657	0.0442	-0.1372	-0.0021	0.1031	0.0066	-0.2501	0.0152	0.3076	-0.0205	0.1701	-0.0125	-0.0432	0.1472	-0.0017	0.2355	34.8621	-4.7771	71.7809
3	0.6492	0.713	0.008	2.1177	-0.9149	1.2007	0.018	-0.0859	0.1155	0.2075	0.1818	0.2999	-0.2099	-0.1949	-0.1094	0.1914	0.0465	0.0367	0.176	0.0411	0.2291	11.5992	9.076	60.5879
4	1.1799	0.1999	-0.002	1.3355	-0.2489	1.018	0.0166	-0.013	-0.2661	-0.0989	0.083	0.3157	0.1504	-0.4045	-0.092	0.2108	-0.0509	-0.0454	0.2107	0.0709	0.2625	8.7317	-15.5342	67.3755
5	1.425	0.5748	0.9021	0.5168	0.0992	0.9522	-0.1928	0.0308	0.3919	0.1831	-0.206	0.7344	-0.0329	-0.2341	0.0228	0.1329	0.0192	-0.0534	0.1983	-0.0953	0.5435	-2.4539	-36.731	63.5216
6	1.452	0.1339	-0.313	1.4837	0.2318	1.544	0.1202	0.6672	0.8809	-0.2479	-0.1998	0.0064	-0.3591	-0.2476	0.0057	0.257	0.0834	-0.0666	0.4392	0.033	0.6752	-19.723	-40.4911	44.0219
7	2.2597	-0.9315	-0.3346	0.7168	-0.0818	0.4904	-0.129	-0.223	-0.144	0.1823	0.0405	0.0791	-0.045	0.132	0.0842	0.1992	-0.0268	-0.012	0.4169	-0.151	0.3359	-39.1816	-43.4654	65.0675
8	1.7	-0.9391	-0.7089	1.4515	0.6117	1.8986	-0.1275	-0.4918	-0.7434	0.3731	0.127	0.1759	0.4361	-0.1515	0.0205	0.3422	-0.0108	-0.0193	0.412	0.0389	0.5389	-19.3507	-60.2841	64.7574
9	0.5064	-0.2975	0.6628	2.0284	-1.5599	1.6765	0.0648	0.052	0.1593	-0.2437	-0.136	-0.2159	0.3205	0.1916	-0.0378	0.2813	0.0331	0.0312	0.2141	0.0128	0.1745	27.575	-61.3177	85.713
10	1.1238	-0.1426	-0.1786	1.378	-0.1615	1.3758	-0.0846	-0.3954	0.1528	0.9122	0.1043	-0.5726	-0.0976	0.2551	0.002	0.6449	0.0577	-0.0981	0.4728	0.0118	0.2109	32.0375	-66.7687	110.5976
11	1.8135	0.3178	0.4516	2.0039	0.3006	1.827	0.1121	-0.0564	-0.3558	0.7496	-0.0065	0.0206	0.4886	-0.0303	-0.1232	0.6725	-0.0371	0.0196	0.3438	0.0762	0.302	20.2045	-92.4256	105.023
12	1.1125	0.1707	-0.0528	1.5811	0.4335	1.0607	0.0442	0.0627	0.0602	0.3512	-0.0344	0.8065	0.0002	-0.5057	0.0047	0.425	0.0143	0.1949	0.4779	0.0316	0.4774	5.2541	-71.4858	100.9562
13	2.4877	0.5314	-0.3699	2.2382	-0.3675	1.297	-0.11	-0.4776	-0.4406	0.0333	-0.0704	-0.5656	0.0284	0.2849	0.0597	0.485	0.0363	-0.0411	0.5965	0.1031	0.4107	-18.4544	-32.4346	100.2597
14	0.55	-0.3642	0.059	1.0086	-0.1217	1.4635	-0.0679	-0.5294	-0.1422	0.4364	0.0083	0.1834	0.1194	-0.1718	0.0734	0.5412	0.0407	0.0905	0.6111	0.0632	0.3669	-43.0034	-32.8009	108.2876
15	2.2026	-0.3695	0.0178	2.3077	0.915	1.2628	-0.1953	0.2764	-0.4784	0.0969	0.0365	0.5149	0.3177	-0.183	0.0884	0.3314	-0.0872	0.0242	0.3902	-0.0605	0.4211	-48.5316	-36.4268	80.1823
16	0.9149	-0.1292	-0.0774	1.2398	-0.3187	1.155	-0.1319	-0.0826	0.559	0.3439	0.135	-0.2722	-0.1869	0.1338	-0.0424	0.3918	-0.0261	-0.0761	0.3851	-0.0779	0.3869	-37.1484	-14.6294	87.2032

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and ((resseq 3:153))
2	X-RAY DIFFRACTION	2	chain 'A' and ((resseq 154:244))
3	X-RAY DIFFRACTION	3	chain 'B' and ((resseq 3:153))
4	X-RAY DIFFRACTION	4	chain 'B' and ((resseq 154:244))
5	X-RAY DIFFRACTION	5	chain 'C' and ((resseq 3:153))
6	X-RAY DIFFRACTION	6	chain 'C' and ((resseq 154:244))
7	X-RAY DIFFRACTION	7	chain 'D' and ((resseq 2:153))
8	X-RAY DIFFRACTION	8	chain 'D' and ((resseq 154:244))
9	X-RAY DIFFRACTION	9	chain 'E' and ((resseq 3:153))
10	X-RAY DIFFRACTION	10	chain 'E' and ((resseq 154:244))
11	X-RAY DIFFRACTION	11	chain 'F' and ((resseq 3:153))
12	X-RAY DIFFRACTION	12	chain 'F' and ((resseq 154:244))
13	X-RAY DIFFRACTION	13	chain 'G' and ((resseq 3:153))
14	X-RAY DIFFRACTION	14	chain 'G' and ((resseq 154:244))
15	X-RAY DIFFRACTION	15	chain 'H' and ((resseq 3:153))
16	X-RAY DIFFRACTION	16	chain 'H' and ((resseq 154:244))

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