PDB-5twj: Crystal Structure of RlmH in Complex with S-Adenosylmethionine

ID or keywords:

Entry

Database: PDB / ID: 5twj

Title

Crystal Structure of RlmH in Complex with S-Adenosylmethionine

Components

Ribosomal RNA large subunit methyltransferase H

Keywords

TRANSFERASE / S-adenosylmethionine / RNA methyltransferase / SPOUT / pseudouridine / helix 69

Function / homology

Function and homology information

23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / rRNA base methylation / rRNA methylation / ribosome binding / protein homodimerization activity / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.299 Å

Authors

Koh, C.S. / Madireddy, R. / Beane, T.J. / Zamore, P.D. / Korostelev, A.A.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM107465	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM106105	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM62862	United States

Citation

Journal: Sci Rep / Year: 2017
Title: Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine.
Authors: Koh, C.S. / Madireddy, R. / Beane, T.J. / Zamore, P.D. / Korostelev, A.A.

History

Deposition	Nov 14, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 4, 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	5twj.cif.gz	269.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5twj.ent.gz	219.6 KB	Display	PDB format
PDBx/mmJSON format	5twj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5twj_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	5twj_full_validation.pdf.gz	1.7 MB	Display
Data in XML	5twj_validation.xml.gz	26.3 KB	Display
Data in CIF	5twj_validation.cif.gz	34.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/5twj ftp://data.pdbj.org/pub/pdb/validation_reports/tw/5twj	HTTPS FTP

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Related structure data

Related structure data	5twkC 1ns5S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5twk-2 5twk-1 3mid-d 5wja-1 1ns5-d 2bkw-d 4bbm-1 2gaa-d 3mie-d 4fak-1 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	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

C: Ribosomal RNA large subunit methyltransferase H

D: Ribosomal RNA large subunit methyltransferase H

A: Ribosomal RNA large subunit methyltransferase H

B: Ribosomal RNA large subunit methyltransferase H

hetero molecules

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

1

C: Ribosomal RNA large subunit methyltransferase H

D: Ribosomal RNA large subunit methyltransferase H

hetero molecules

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

2

A: Ribosomal RNA large subunit methyltransferase H

B: Ribosomal RNA large subunit methyltransferase H

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.530, 37.360, 122.070
Angle α, β, γ (deg.)	90.00, 104.99, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Ribosomal RNA large subunit methyltransferase H / 23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA ...23S rRNA (pseudouridine1915-N3)-methyltransferase / 23S rRNA m3Psi1915 methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase RlmH Mass: 18293.111 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rlmH / Production host: Escherichia coli (E. coli) References: UniProt: B7MFQ9, UniProt: P0A8I8*PLUS, 23S rRNA (pseudouridine1915-N3)-methyltransferase
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / 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 Å³/Da / Density % sol: 38.58 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-bicine buffer (pH 8.5), 0.09 M NaF, 0.09 M NaBr, 0.09 M NaI, 20% v/v PEG 550 MME, 10% w/v PEG 20,000 in the presence of 2 mM S-Adenosylmethionine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.299→29.5 Å / Num. obs: 26034 / % possible obs: 98.59 % / Redundancy: 5.5 % / CC_1/2: 0.999 / R_merge(I) obs: 0.077 / Net I/σ(I): 14.46
Reflection shell	Resolution: 2.3→2.38 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.755 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2583 / CC_1/2: 0.742 / % possible all: 98.47

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1NS5

1ns5

Resolution: 2.299→29.479 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2287	1298	4.99 %
R_work	0.1771	-	-
obs	0.1798	26018	98.53 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.299→29.479 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4960	0	108	94	5162

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5204
X-RAY DIFFRACTION	f_angle_d	1.318	7080
X-RAY DIFFRACTION	f_dihedral_angle_d	15.286	1972
X-RAY DIFFRACTION	f_chiral_restr	0.056	780
X-RAY DIFFRACTION	f_plane_restr	0.006	892

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 (%)
2.299-2.391	0.2953	141	0.2345	2722	X-RAY DIFFRACTION	98
2.391-2.4998	0.2861	144	0.2397	2725	X-RAY DIFFRACTION	99
2.4998-2.6315	0.3132	143	0.2313	2722	X-RAY DIFFRACTION	99
2.6315-2.7963	0.3141	141	0.2204	2683	X-RAY DIFFRACTION	98
2.7963-3.012	0.253	144	0.2143	2749	X-RAY DIFFRACTION	99
3.012-3.3147	0.2581	147	0.1995	2781	X-RAY DIFFRACTION	100
3.3147-3.7935	0.2573	146	0.1709	2758	X-RAY DIFFRACTION	99
3.7935-4.7761	0.1872	144	0.1408	2753	X-RAY DIFFRACTION	98
4.7761-29.4814	0.1709	148	0.1501	2827	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	3.1491	-0.9499	1.5941	5.3276	-2.6706	2.8101	-0.1173	-0.6483	0.3218	0.2927	-0.0526	-0.6064	-1.0443	0.5689	0.0805	0.4603	-0.1424	-0.0409	0.7357	-0.0924	0.5247	4.2712	13.8564	58.0115
2	3.7799	-0.0584	0.3778	5.5245	-2.8325	2.0601	-0.1759	-0.4382	0.7846	0.0859	-0.275	0.3463	-1.2221	0.2878	0.56	0.6666	-0.0184	0.0311	0.3079	-0.0875	0.5447	-3.9539	18.9918	49.9558
3	6.2291	-0.207	1.423	2.6539	-1.7734	1.4756	0.0018	-0.9707	0.2501	0.206	0.4437	-0.7264	-1.3084	0.7427	0.2691	0.746	-0.4001	0.1823	0.7147	-0.4291	0.7828	-0.0511	15.442	60.7458
4	0.4157	0.4391	0.6452	2.6617	0.6389	2.2121	0.7489	-2.1992	0.038	-0.3757	-0.2375	-0.6136	-0.7687	1.8172	-0.0634	0.5511	-0.1773	0.1063	1.5078	0.0273	0.7147	21.1371	8.0887	50.6745
5	5.6198	-1.668	2.8798	5.3317	0.2407	5.203	0.2893	-1.028	-0.3062	0.43	-0.4655	-0.3764	0.2066	1.2042	0.0342	0.447	-0.0263	0.04	0.7288	0.1714	0.4145	3.4905	-0.0694	57.3985
6	5.205	3.0065	3.2749	2.5157	3.1908	4.3457	0.4469	-1.5209	-0.3485	0.5899	-0.3276	-0.16	1.1502	0.299	-0.0652	0.44	-0.0075	0.0241	0.5277	0.0197	0.381	-5.8588	1.025	63.7553
7	2.2781	-0.5619	0.5925	6.0211	-0.4171	6.6647	-0.1441	-1.5758	0.3122	0.2452	-0.0954	-0.5723	0.1283	1.456	0.3681	0.3922	-0.0491	-0.0147	0.8715	0.0398	0.4208	8.6028	5.6996	56.6324
8	4.2743	-0.5389	-2.3096	1.769	-0.8113	4.7017	-0.1021	-0.6635	-0.1689	0.3007	-0.1795	-0.1899	-0.0698	0.6921	0.2311	0.3828	-0.0169	-0.0157	0.3137	0.0162	0.3017	-0.1877	4.9091	52.8919
9	3.765	1.9712	-2.5152	3.3296	1.0931	4.175	-0.2225	0.2513	-0.142	0.3272	-0.0983	1.2041	1.2489	-0.2687	0.147	0.5322	0.073	0.0465	0.4218	-0.0299	0.4251	-18.2625	10.0013	56.8286
10	5.3599	1.0276	0.4279	6.4197	1.4868	6.1342	0.1677	0.6025	0.7144	-0.337	-0.007	-0.1287	-1.019	-0.4128	-0.1872	0.4688	0.0502	0.0133	0.2817	0.1213	0.4107	-7.9079	13.0833	32.3691
11	4.9624	-0.0182	-4.3236	0.9144	0.8354	4.5774	-0.0907	0.8431	-0.1661	-0.4732	0.192	-0.0912	-0.2026	-0.565	-0.1669	0.5959	0.0522	-0.0349	0.6129	0.1381	0.4566	-7.5971	9.944	26.0696
12	9.6776	-2.6748	-3.2732	7.4465	-1.3698	3.4531	0.2562	-0.7414	-0.1045	0.907	-0.7509	-0.4817	-0.3418	-1.5238	0.6544	0.6733	0.0627	-0.0041	1.4366	-0.077	0.8094	-30.8752	9.9996	43.8466
13	3.9619	-0.2231	-0.9416	2.7036	0.4085	5.7057	0.0585	0.5156	-0.1614	-0.4301	-0.117	0.1341	0.3943	-0.5765	0.0878	0.4277	0.0323	-0.0193	0.2957	0.0169	0.2803	-11.3799	0.434	33.9979
14	7.8798	0.2109	-0.6033	3.2962	2.5801	2.79	0.1565	-0.5209	0.3214	-0.4788	-0.4644	-1.9704	0.9947	2.5175	0.2448	0.8338	0.0673	0.0203	1.075	0.2271	1.03	11.3162	6.0398	31.8206
15	3.8751	-2.0341	-1.1503	5.85	-1.033	5.6072	0.1893	-0.6391	0.7867	1.3663	-0.3954	-0.9097	-0.713	0.3971	0.1449	0.7384	-0.2031	-0.2089	0.9344	0.1073	0.7443	26.2126	28.2174	30.8274
16	8.8454	2.7826	-4.2204	6.0209	-0.3349	2.6094	0.9659	-1.2276	1.6494	0.3491	-0.3337	0.3952	-0.9598	0.304	-0.4994	0.5787	-0.0561	-0.0119	0.4423	-0.075	0.7592	19.6943	34.9786	22.3819
17	6.4819	-0.039	-0.5396	1.0774	-1.3894	1.7519	0.6416	-1.6225	-0.8741	0.7112	-0.9858	0.0847	-0.3021	0.0735	0.2765	0.9951	-0.3148	-0.1034	1.0788	-0.1303	0.9097	21.1005	29.5817	32.9619
18	2.8217	0.8462	-1.3709	0.4936	-0.9551	2.927	0.2988	-0.0738	-0.0882	-0.4967	-0.4661	-1.003	0.0737	0.4873	-0.5229	0.7577	-0.1234	0.1972	1.1671	-0.1179	1.2373	46.7545	26.2064	19.2575
19	0.2912	0.2878	0.8756	2.9767	1.0123	2.68	0.5675	-1.0989	-0.6518	0.5716	-0.513	-1.1893	0.0248	0.968	0.0953	0.633	-0.1434	-0.2177	0.9882	0.2843	0.8515	33.2379	17.9845	28.3181
20	4.4551	-0.8736	0.8582	3.4178	0.6919	3.699	0.3939	-1.9011	-0.9104	0.6441	-0.6124	-0.1393	0.3538	0.3449	0.2479	0.6259	-0.1981	-0.0967	0.6914	0.1957	0.5263	21.8028	17.5513	30.6785
21	4.6159	-0.0088	-0.1925	3.1755	0.2336	3.1769	0.1	-0.7182	-0.3782	0.4069	-0.2626	-0.4744	0.0614	0.488	0.1342	0.5102	-0.0347	-0.0972	0.4667	0.117	0.5053	22.3939	20.4702	23.4438
22	3.455	1.9031	-0.7141	9.6466	2.7481	2.7522	0.4785	-0.0246	-0.266	0.5551	-0.351	1.0772	0.9364	-1.3814	-0.0976	0.5326	0.0007	-0.0462	0.6822	0.0061	0.5888	3.9842	25.6655	24.3246
23	6.3445	2.2817	2.6446	6.6786	-2.1624	4.4328	0.1402	1.1606	0.5457	-0.7032	-0.0574	-0.2004	0.0058	-0.7712	-0.4157	0.5033	0.0936	0.0198	0.5409	0.186	0.5628	15.0147	28.9081	-0.8024
24	3.3945	2.7775	0.243	4.1375	-1.997	2.6535	0.4356	0.5396	0.7341	-0.6793	0.0295	-0.7032	-1.3626	0.6653	-0.6705	0.6931	-0.0637	0.0238	0.6334	0.0937	0.7821	22.2477	34.9763	7.7121
25	7.888	-0.9919	-2.6865	3.1625	1.6488	7.4649	0.1092	1.1083	0.4497	-0.9674	0.0603	-0.8026	-1.3803	0.6335	0.0153	0.8298	-0.0557	0.1766	1.0063	0.2073	0.8454	20.1242	29.8714	-2.9869
26	2.0042	1.3008	1.7571	7.9374	-4.3602	6.3354	-0.1467	0.2588	-0.227	1.0167	-0.6142	0.5758	-0.5419	-2.2208	1.0169	0.7714	0.0916	0.1753	1.2921	-0.1449	0.8708	-5.6821	29.1235	10.9451
27	6.5693	-1.1128	0.8567	4.1645	0.3944	5.5506	-0.0113	1.0634	0.0153	-0.4498	-0.3552	0.7007	-0.0512	-1.9908	0.2529	0.5566	0.0365	-0.1296	0.9286	-0.0998	0.4575	-0.7695	24.0689	1.1254
28	5.9822	-0.5665	1.0224	4.8341	-0.5033	7.6625	0.2413	0.7941	-0.3299	-0.376	-0.5356	-0.0962	0.7511	0.2079	0.1344	0.4931	0.0265	0.0071	0.5544	-0.083	0.454	14.9696	15.3848	1.9505
29	7.0947	-2.0456	1.8792	4.661	-0.5584	2.736	0.1242	1.7341	-1.0189	-1.0544	0.1083	-0.3563	1.1742	0.3459	0.1712	0.523	0.0567	0.1129	0.777	-0.0686	0.7291	25.1825	14.9092	-2.915
30	5.8855	-0.7127	0.2276	3.194	0.1619	7.4344	0.0902	0.8304	-0.3279	-0.1071	-0.2154	0.0766	0.2064	-0.6106	0.2588	0.4349	0.0072	-0.0108	0.4199	-0.0588	0.4468	11.1693	18.516	4.1608
31	6.1882	0.1572	1.806	7.2171	-0.3666	2.4498	0.0113	0.9542	0.1425	-0.4604	-0.2619	-0.6227	-0.5596	0.9356	0.1798	0.4715	0.0019	0.0042	0.6757	0.0752	0.511	24.5195	24.7445	5.9719
32	2.1693	1.8266	-0.5468	6.1217	0.0709	7.641	-0.4006	2.7512	0.5695	-0.0114	0.3074	-1.0614	1.4071	0.9683	0.3673	0.9826	0.2455	0.202	1.6713	0.3431	1.009	37.2064	25.1234	6.9754

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid -1 through 13 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 14 through 26 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 27 through 38 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 39 through 64 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 65 through 80 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 81 through 94 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 95 through 109 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 110 through 147 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 148 through 155 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid -1 through 26 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 27 through 38 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 39 through 48 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 49 through 147 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 148 through 155 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid -1 through 13 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 14 through 26 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 27 through 38 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 39 through 48 )
19	X-RAY DIFFRACTION	19	chain 'A' and (resid 49 through 80 )
20	X-RAY DIFFRACTION	20	chain 'A' and (resid 81 through 109 )
21	X-RAY DIFFRACTION	21	chain 'A' and (resid 110 through 147 )
22	X-RAY DIFFRACTION	22	chain 'A' and (resid 148 through 155 )
23	X-RAY DIFFRACTION	23	chain 'B' and (resid -1 through 13 )
24	X-RAY DIFFRACTION	24	chain 'B' and (resid 14 through 26 )
25	X-RAY DIFFRACTION	25	chain 'B' and (resid 27 through 38 )
26	X-RAY DIFFRACTION	26	chain 'B' and (resid 39 through 48 )
27	X-RAY DIFFRACTION	27	chain 'B' and (resid 49 through 64 )
28	X-RAY DIFFRACTION	28	chain 'B' and (resid 65 through 80 )
29	X-RAY DIFFRACTION	29	chain 'B' and (resid 81 through 94 )
30	X-RAY DIFFRACTION	30	chain 'B' and (resid 95 through 128 )
31	X-RAY DIFFRACTION	31	chain 'B' and (resid 129 through 148 )
32	X-RAY DIFFRACTION	32	chain 'B' and (resid 149 through 155 )

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