PDB-3m6v: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus ...

ID or keywords:

Entry

Database: PDB / ID: 3m6v

Title

Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus in space group P2 in complex with S-Adenosyl-L-Methionine

Components

rRNA methylase

Keywords

TRANSFERASE / rRNA methyltransferase /

5-methylcytidine /

RsmF /

AdoMet / multi-specific /

methyltransferase

Function / homology

Function and homology information

16S rRNA (cytosine1407-C5)-methyltransferase / RNA methyltransferase activity /

RNA methylation /

Transferases; Transferring one-carbon groups; Methyltransferases / rRNA processing /

RNA binding /

cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.82 Å

Authors

Demirci, H. / Larsen, H.G.L. / Hansen, T. / Rasmussen, A. / Cadambi, A. / Gregory, S.T. / Kirpekar, F. / Jogl, G.

Citation

Journal: Rna / Year: 2010
Title: Multi-site-specific 16S rRNA methyltransferase RsmF from Thermus thermophilus.
Authors: Demirci, H. / Larsen, L.H. / Hansen, T. / Rasmussen, A. / Cadambi, A. / Gregory, S.T. / Kirpekar, F. / Jogl, G.

History

Deposition	Mar 16, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 31, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software
Revision 1.3	Sep 6, 2023	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 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3m6v.cif.gz	383.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3m6v.ent.gz	309.5 KB	Display	PDB format
PDBx/mmJSON format	3m6v.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/m6/3m6v ftp://data.pdbj.org/pub/pdb/validation_reports/m6/3m6v	HTTPS FTP

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Related structure data

Related structure data	3m6uSC 3m6wC 3m6xC 2frx S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3uxv-1 3m6w-d 5flv-3 2v64-3 6mv1-d 2xii-2 4rag-d 1fs0-d 3fxk-d 3m6u-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

A: rRNA methylase

B: rRNA methylase

hetero molecules

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

1

A: rRNA methylase

hetero molecules

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

2

B: rRNA methylase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.956, 78.316, 108.122
Angle α, β, γ (deg.)	90.000, 107.050, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	rRNA methylase Mass: 50878.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: RsmF minus / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1387 / Plasmid: pLJ102 / Production host: Escherichia coli (E. coli) / Strain (production host): CP79 References: UniProt: Q5SII2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1285 / 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: 2.62 Å³/Da / Density % sol: 53.12 %
Crystal grow	Temperature: 277 K / pH: 7.5 Details: 200 mM NaCl, 12% w/v PEG8000 and 100 mM HEPES-KOH (pH7.5), microbatch under oil, temperature 277K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X4C / Wavelength: 0.98 Å

Detector

Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2008 / Details: Slits: Variable vertical and horizontal slits

Radiation

Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Redundancy: 2.8 % / Av σ(I) over netI: 12.64 / Number: 262022 / R_merge(I) obs: 0.082 / Χ²: 1.04 / D res high: 1.82 Å / D res low: 30 Å / Num. obs: 93014 / % possible obs: 97

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.92	30	95.3	1	0.055	1.018	3
3.11	3.92	97.3	1	0.062	0.992	3
2.72	3.11	98	1	0.078	1.037	3
2.47	2.72	98.4	1	0.096	1.074	3
2.29	2.47	98.8	1	0.121	1.041	2.9
2.16	2.29	99.1	1	0.142	1.059	2.9
2.05	2.16	99.2	1	0.181	1.081	2.9
1.96	2.05	99.2	1	0.233	1.08	2.8
1.89	1.96	97.7	1	0.289	1.019	2.5
1.82	1.89	86.5	1	0.38	0.941	2

Reflection

Resolution: 1.82→30 Å / Num. obs: 93014 / % possible obs: 97 % / Redundancy: 2.8 % / R_merge(I) obs: 0.082 / Χ²: 1.04 / Net I/σ(I): 8.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.82-1.89	2	0.38	8237	0.941	86.5
1.89-1.96	2.5	0.289	9333	1.019	97.7
1.96-2.05	2.8	0.233	9451	1.08	99.2
2.05-2.16	2.9	0.181	9482	1.081	99.2
2.16-2.29	2.9	0.142	9508	1.059	99.1
2.29-2.47	2.9	0.121	9457	1.041	98.8
2.47-2.72	3	0.096	9416	1.074	98.4
2.72-3.11	3	0.078	9431	1.037	98
3.11-3.92	3	0.062	9391	0.992	97.3
3.92-30	3	0.055	9308	1.018	95.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.5_2	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M6U

3m6u

Resolution: 1.82→29.068 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.891 / SU ML: 0.22 / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.194	4616	5.03 %
R_work	0.162	-	-
obs	0.164	91762	97.29 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 37.155 Å² / k_sol: 0.332 e/Å³

Displacement parameters

B_iso max: 94.37 Å² / B_iso mean: 23.235 Å² / B_iso min: 5.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.422 Å²	-0 Å²	-0.178 Å²
2-	-	0.308 Å²	0 Å²
3-	-	-	0.114 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→29.068 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7084	0	54	1285	8423

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7396
X-RAY DIFFRACTION	f_angle_d	1.038	10067
X-RAY DIFFRACTION	f_chiral_restr	0.066	1053
X-RAY DIFFRACTION	f_plane_restr	0.005	1329
X-RAY DIFFRACTION	f_dihedral_angle_d	16.731	2755

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.82-1.841	0.259	114	0.222	2469	2583	84
1.841-1.862	0.261	143	0.217	2718	2861	90
1.862-1.885	0.23	165	0.208	2802	2967	95
1.885-1.909	0.249	125	0.198	2879	3004	97
1.909-1.934	0.238	154	0.177	2955	3109	98
1.934-1.961	0.216	124	0.179	2938	3062	99
1.961-1.988	0.247	146	0.175	2951	3097	99
1.988-2.018	0.214	188	0.166	2925	3113	99
2.018-2.05	0.216	169	0.163	2980	3149	99
2.05-2.083	0.176	165	0.163	2904	3069	99
2.083-2.119	0.209	165	0.156	2960	3125	99
2.119-2.158	0.203	151	0.156	2956	3107	99
2.158-2.199	0.19	158	0.149	2940	3098	99
2.199-2.244	0.203	161	0.151	2942	3103	99
2.244-2.293	0.201	176	0.157	2934	3110	99
2.293-2.346	0.185	153	0.156	2932	3085	99
2.346-2.405	0.193	157	0.157	2927	3084	99
2.405-2.47	0.185	157	0.16	2973	3130	99
2.47-2.543	0.214	152	0.157	2961	3113	99
2.543-2.625	0.219	191	0.16	2891	3082	98
2.625-2.718	0.195	183	0.154	2895	3078	98
2.718-2.827	0.167	145	0.156	2919	3064	98
2.827-2.955	0.207	132	0.156	2971	3103	98
2.955-3.111	0.178	163	0.159	2938	3101	98
3.111-3.306	0.19	160	0.157	2913	3073	98
3.306-3.561	0.154	134	0.154	2926	3060	97
3.561-3.918	0.19	139	0.139	2949	3088	97
3.918-4.483	0.145	159	0.129	2878	3037	96
4.483-5.642	0.136	139	0.14	2923	3062	96
5.642-29.072	0.178	148	0.162	2897	3045	94

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	0.0577	0.0132	-0.1724	0.0565	-0.1085	0.6349	-0.0125	-0.0056	-0.0188	0.0373	-0.0271	0.004	-0.0966	-0.0336	0.0315	0.0391	0.0025	-0.0028	0.0348	0.0018	0.0496	13.6942	18.2297	40.1384
2	0.0612	-0.0419	0.0537	0.5079	-0.1577	0.1631	0.0209	-0.018	-0.0247	-0.1152	-0.062	-0.0091	0.035	-0.0093	0.0329	0.0297	0.0127	0.0052	0.0172	0.0045	0.0204	19.868	6.6417	28.231
3	0.1296	-0.0407	0.1037	0.3168	-0.1381	0.1288	0.0321	-0.0634	-0.0199	-0.0389	-0.0695	-0.0232	0.0352	-0.0019	0.0294	0.0638	0.0038	-0.0032	0.0748	0.0156	0.0821	19.5939	-2.5155	42.1844
4	0.3648	-0.0318	-0.2294	0.0145	0.0929	0.6103	0.0931	0.0519	0.0998	0.0061	-0.0404	0.0073	0.0916	0.0562	-0.0365	0.2143	0.0752	0.0989	0.0902	0.0184	0.1229	36.9744	7.4443	4.5651
5	0.1058	-0.0063	-0.0213	0.1302	-0.2339	0.5108	-0.0377	0.0204	-0.0184	-0.0202	-0.0152	0.0269	0.0488	0.0383	0.0454	0.093	0.0041	0.0344	0.0235	-0.0002	0.0412	26.8946	18.7893	10.205
6	0.18	-0.1439	0.0724	0.1348	-0.0101	0.1754	-0.0592	-0.0471	-0.0089	0.0294	0.0372	0.0215	-0.0778	-0.0616	0.0119	0.01	0.0215	0.0036	0.0297	-0	0.0319	-15.8266	-16.2146	38.7724
7	0.1085	-0.0998	0.0976	0.0896	-0.0918	0.1131	0.031	0.0162	-0.0301	-0.0243	-0.0285	0.0633	0.0236	0.0037	-0.0152	-0.1014	0.0522	-0.0878	-0.0066	0.0191	-0.0303	-5.1642	-25.6634	28.2272
8	0.1083	-0.109	0.1384	0.1326	-0.0853	0.2387	0.0114	-0.1002	-0.0388	0.0299	0.0165	0.024	0.0179	0.0226	-0.0237	0.0165	0.0101	-0.0014	0.0531	-0.0008	0.0359	-1.4719	-32.1144	43.1199
9	0.2474	-0.4952	0.7253	0.9941	-1.4577	2.1393	0.1792	0.2232	0.0979	-0.3719	-0.4628	-0.2236	0.5115	0.5424	0.2914	0.2046	0.1696	0.113	0.2815	0.1031	0.1011	11.2919	-21.3129	4.6377
10	0.4623	-0.5226	0.5678	0.8473	-0.786	0.77	0.0709	0.1185	0.014	-0.1826	-0.103	-0.0075	0.0656	0.1435	0.0278	0.0957	0.0207	-0.0107	0.0616	-0.0025	0.035	-2.8055	-13.807	8.6133

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain A and resseq 2:71	A	2 - 71
2	X-RAY DIFFRACTION	2	chain A and resseq 72:198	A	72 - 198
3	X-RAY DIFFRACTION	3	chain A and resseq 201:310	A	201 - 310
4	X-RAY DIFFRACTION	4	chain A and resseq 311:341	A	311 - 341
5	X-RAY DIFFRACTION	5	chain A and resseq 342:459	A	342 - 459
6	X-RAY DIFFRACTION	6	chain B and resseq 2:71	B	2 - 71
7	X-RAY DIFFRACTION	7	chain B and resseq 72:198	B	72 - 198
8	X-RAY DIFFRACTION	8	chain B and resseq 204:309	B	204 - 309
9	X-RAY DIFFRACTION	9	chain B and resseq 310:341	B	310 - 341
10	X-RAY DIFFRACTION	10	chain B and resseq 342:459	B	342 - 459

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