PDB-3g8a: T. thermophilus 16S rRNA G527 methyltransferase in complex with A...

ID or keywords:

Entry

Database: PDB / ID: 3g8a

Title

T. thermophilus 16S rRNA G527 methyltransferase in complex with AdoHcy in space group P61

Components

Ribosomal RNA small subunit methyltransferase G

Keywords

TRANSFERASE / Methyltransferase / 16S rRNA methyltransferase / translation / rRNA processing / S-adenosyl-L-methionine

Function / homology

Function and homology information

16S rRNA (guanine527-N7)-methyltransferase / rRNA (guanine-N7-)-methyltransferase activity / cytosol
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.1 Å

Authors

Demirci, H. / Gregory, S.T. / Belardinelli, R. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G.

Citation

Journal: Rna / Year: 2009
Title: Structural and functional studies of the Thermus thermophilus 16S rRNA methyltransferase RsmG
Authors: Gregory, S.T. / Demirci, H. / Belardinelli, R. / Monshupanee, T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G.

History

Deposition	Feb 11, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 30, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Jul 24, 2019	Group: Data collection / Derived calculations / Refinement description Category: software / struct_conn Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3g8a.cif.gz	580.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3g8a.ent.gz	498 KB	Display	PDB format
PDBx/mmJSON format	3g8a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3g8a_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	3g8a_full_validation.pdf.gz	1.9 MB	Display
Data in XML	3g8a_validation.xml.gz	68.4 KB	Display
Data in CIF	3g8a_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g8/3g8a ftp://data.pdbj.org/pub/pdb/validation_reports/g8/3g8a	HTTPS FTP

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Related structure data

Related structure data	3g88C 3g89C 3g8bC C: citing same article (ref.)
Similar structure data	3g88-2 3g89-1 5hpq-d 3g89-2 3phj-1 3g88-1 4h5f-2 6q7o-d 5fit-1 6wh2-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

3g88C

3g89C

3g8bC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribosomal RNA small subunit methyltransferase G

B: Ribosomal RNA small subunit methyltransferase G

C: Ribosomal RNA small subunit methyltransferase G

D: Ribosomal RNA small subunit methyltransferase G

E: Ribosomal RNA small subunit methyltransferase G

F: Ribosomal RNA small subunit methyltransferase G

hetero molecules

164 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Ribosomal RNA small subunit methyltransferase G

hetero molecules

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

2

B: Ribosomal RNA small subunit methyltransferase G

hetero molecules

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

3

C: Ribosomal RNA small subunit methyltransferase G

hetero molecules

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

4

D: Ribosomal RNA small subunit methyltransferase G

hetero molecules

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

5

E: Ribosomal RNA small subunit methyltransferase G

hetero molecules

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

6

F: Ribosomal RNA small subunit methyltransferase G

hetero molecules

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

Unit cell

Length a, b, c (Å)	134.849, 134.849, 167.139
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Ribosomal RNA small subunit methyltransferase G / 16S rRNA 7-methylguanosine methyltransferase / 16S rRNA m7G methyltransferase / Glucose-inhibited ...16S rRNA 7-methylguanosine methyltransferase / 16S rRNA m7G methyltransferase / Glucose-inhibited division protein B Mass: 26884.688 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: gidB, rsmG, TTHA1971 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)Star References: UniProt: Q9LCY2, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1347 / 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: 2.74 Å³/Da / Density % sol: 55.06 %
Crystal grow	Temperature: 277 K / pH: 8 Details: containing 20% (w/v) PEG1000, 100 mM imidazole (pH 8.0) and 200 mM calcium acetate, microbatch technique under oil, temperature 277K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9797
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9797 Å / Relative weight: 1
Reflection	Resolution: 2.1→25 Å / Num. obs: 98926 / % possible obs: 98.9 % / Redundancy: 4.9 % / R_merge(I) obs: 0.099
Reflection shell	Resolution: 2.1→2.18 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.489 / Mean I/σ(I) obs: 3.14 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.006	data extraction
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing
REFMAC		refinement

Refinement

Resolution: 2.1→24.14 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.29 / σ(F): 1.34 / Phase error: 23.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.229	4940	5 %
R_work	0.174	-	-
obs	0.177	98820	98.8 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.39 Å² / k_sol: 0.36 e/Å³

Displacement parameters

B_iso mean: 38.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.53 Å²	0 Å²	0 Å²
2-	-	-1.53 Å²	0 Å²
3-	-	-	3.059 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→24.14 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10909	0	156	1347	12412

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	11499
X-RAY DIFFRACTION	f_angle_d	1.327	15650
X-RAY DIFFRACTION	f_dihedral_angle_d	17.007	4454
X-RAY DIFFRACTION	f_chiral_restr	0.072	1797
X-RAY DIFFRACTION	f_plane_restr	0.007	2027

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 (%)
2.1-2.1245	0.2798	152	0.213	3137	X-RAY DIFFRACTION	99
2.1245-2.1495	0.2475	169	0.1868	3115	X-RAY DIFFRACTION	100
2.1495-2.1757	0.1995	184	0.173	3200	X-RAY DIFFRACTION	100
2.1757-2.2032	0.2344	175	0.1718	3113	X-RAY DIFFRACTION	100
2.2032-2.2322	0.2289	160	0.165	3146	X-RAY DIFFRACTION	100
2.2322-2.2628	0.2408	165	0.1724	3157	X-RAY DIFFRACTION	100
2.2628-2.2951	0.224	182	0.1743	3142	X-RAY DIFFRACTION	100
2.2951-2.3293	0.2436	186	0.1553	3125	X-RAY DIFFRACTION	100
2.3293-2.3657	0.2198	154	0.1637	3176	X-RAY DIFFRACTION	100
2.3657-2.4044	0.2617	162	0.1688	3179	X-RAY DIFFRACTION	100
2.4044-2.4458	0.2383	176	0.1692	3136	X-RAY DIFFRACTION	100
2.4458-2.4903	0.2388	155	0.1694	3153	X-RAY DIFFRACTION	100
2.4903-2.5381	0.2428	157	0.167	3176	X-RAY DIFFRACTION	100
2.5381-2.5899	0.2571	157	0.1762	3181	X-RAY DIFFRACTION	100
2.5899-2.6461	0.2584	167	0.1776	3162	X-RAY DIFFRACTION	100
2.6461-2.7076	0.2474	139	0.1753	3148	X-RAY DIFFRACTION	100
2.7076-2.7752	0.2195	155	0.1811	3147	X-RAY DIFFRACTION	100
2.7752-2.8501	0.2572	183	0.1753	3150	X-RAY DIFFRACTION	100
2.8501-2.9338	0.2384	164	0.1823	3156	X-RAY DIFFRACTION	99
2.9338-3.0284	0.2548	169	0.1938	3154	X-RAY DIFFRACTION	100
3.0284-3.1364	0.2941	173	0.1903	3119	X-RAY DIFFRACTION	99
3.1364-3.2617	0.204	154	0.1738	3153	X-RAY DIFFRACTION	99
3.2617-3.4097	0.2092	152	0.1622	3145	X-RAY DIFFRACTION	99
3.4097-3.589	0.2107	174	0.1664	3110	X-RAY DIFFRACTION	99
3.589-3.813	0.2077	156	0.1618	3142	X-RAY DIFFRACTION	99
3.813-4.1061	0.2089	168	0.1537	3112	X-RAY DIFFRACTION	98
4.1061-4.5169	0.1714	168	0.1367	3088	X-RAY DIFFRACTION	98
4.5169-5.1649	0.189	165	0.1424	3086	X-RAY DIFFRACTION	97
5.1649-6.4863	0.2275	169	0.1927	3053	X-RAY DIFFRACTION	96
6.4863-24.1466	0.2657	150	0.2024	2819	X-RAY DIFFRACTION	88

Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

ID	Method	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	refined	1.0784	1.0212	-0.7281	2.1735	-1.5679	0.1179	-0.068	-0.0572	-0.2322	-0.3778	-0.1612	-0.8274	0.1503	0.305	0.2318	0.3109	-0.0017	0.1527	0.2534	-0.0006	0.4069	18.3633	89.2757	-10.6789
2		1.827	1.4817	-0.4232	1.4538	-0.2146	0.3643	-0.1605	0.1928	-0.1382	-0.3475	0.0741	-0.2117	-0.015	0.043	0.0676	0.3244	0.024	0.0623	0.1902	-0.0254	0.1984
3		1.9944	-1.1457	0.1418	2.4285	0.5563	1.2344	0.0677	0.0305	-0.1236	-0.1639	-0.1723	0.3789	-0.0588	-0.2172	0.0795	0.2439	0.0219	0.0049	0.1861	-0.0229	0.157
4		1.8374	0.0924	-0.6787	0.9552	0.0217	0.2137	-0.184	-0.2772	-0.3336	0.0041	0.0599	0.1377	0.1496	0.0007	0.0756	0.2193	0.0312	0.0292	0.237	0.0796	0.2538
5		2.3333	0.4724	-0.2741	1.0408	-0.6296	-0.5655	0.0129	-0.1516	-0.121	-0.0135	-0.0266	-0.0388	0.0562	-0.008	0.0193	0.2031	0.0373	-0.0055	0.2249	0.0131	0.1614
6		1.6756	0.4172	0.1963	2.6038	0.1059	0.7153	-0.1401	0.0241	0.2332	0.0622	0.0868	-0.0786	-0.1544	0.129	0.0465	0.2229	-0.0075	-0.028	0.2128	0.0222	0.1726
7		1.0049	-0.839	-0.2342	2.5314	0.4938	0.3069	0.0187	0.115	-0.0983	0.3682	-0.0765	0.6957	-0.0381	-0.2509	0.0158	0.2957	0.0086	0.0754	0.2497	0.0583	0.3489
8		1.6158	-0.4395	-0.007	1.9577	-0.394	0.1114	-0.1689	-0.172	-0.1038	0.2732	0.1003	0.0921	-0.0871	-0.0732	0.0561	0.2699	-0.0027	0.0095	0.214	0.0378	0.1837
9		2.6136	0.889	-0.7577	1.8535	-0.25	1.6766	-0.0345	-0.1049	-0.0938	0.1025	-0.132	-0.2696	-0.0315	0.2146	0.1597	0.1952	-0.0413	-0.0237	0.1832	0.0672	0.1526
10		1.8871	0.4473	-0.4503	1.2088	0.3542	1.53	-0.2531	0.1773	-0.5328	-0.0729	0.1813	-0.3565	0.0138	0.3422	-0.0391	0.2348	0.0053	-0.0153	0.3043	-0.0908	0.3352
11		2.2726	-0.1536	0.501	1.5045	0.16	0.0438	0.0381	0.3484	-0.1691	-0.0819	-0.0375	0.0361	0.0185	0.1174	-0.0087	0.2176	-0.0216	-0.0288	0.249	-0.0329	0.1702
12		1.7588	0.4288	0.2128	2.7711	0.8418	1.372	-0.1382	0.0255	0.2175	-0.1293	-0.0335	0.1749	-0.185	-0.0472	0.164	0.2172	-0.0288	-0.0596	0.1682	-0.0067	0.161
13		1.0529	1.2227	1.0543	2.1457	1.2659	0.3833	0.1444	-0.2345	0.7879	0.0072	-0.3597	0.6548	-0.1657	-0.1886	0.2264	0.2142	-0.0233	0.0918	0.2601	-0.1338	0.4116
14		1.4876	0.7006	-0.254	2.7349	0.4467	-0.1046	0.0962	-0.2043	0.1108	0.362	-0.1664	0.2146	-0.0524	-0.0655	0.0597	0.2193	-0.0545	0.0599	0.2838	-0.0433	0.1674
15		2.8549	-0.1809	-0.2845	2.1724	0.0851	0.9744	-0.0241	-0.2707	-0.33	0.0253	-0.0307	-0.1915	0.1377	0.1898	0.0505	0.1556	-0.0209	0.0239	0.2414	0.0112	0.1519
16		0.931	0.6317	-0.1026	1.2984	-0.5075	0.0736	-0.1225	0.0335	-0.0633	-0.2395	0.0092	-0.3178	0.0407	0.0508	0.0887	0.2403	0.0159	0.0611	0.1929	-0.0034	0.2776
17		1.8105	0.8404	-0.544	1.0281	-0.0015	0.0887	-0.1269	0.052	-0.1311	-0.1222	0.094	-0.0668	0.0353	0.0597	0.0234	0.2609	0.0114	0.0049	0.1803	-0.0122	0.186
18		2.8092	-0.6553	0.1876	2.1312	0.3834	0.9792	0.114	-0.0754	0.0214	-0.0314	-0.1648	0.2546	0.0106	-0.1839	0.043	0.1827	0.0112	0.0148	0.1855	-0.0166	0.157

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 1:42	A	1 - 42
2	X-RAY DIFFRACTION	2	chain A and resseq 43:137	A	43 - 137
3	X-RAY DIFFRACTION	3	chain A and resseq 138:249	A	138 - 249
4	X-RAY DIFFRACTION	4	chain B and resseq 1:42	B	1 - 42
5	X-RAY DIFFRACTION	5	chain B and resseq 43:137	B	43 - 137
6	X-RAY DIFFRACTION	6	chain B and resseq 138:249	B	138 - 249
7	X-RAY DIFFRACTION	7	chain C and resseq 1:42	C	1 - 42
8	X-RAY DIFFRACTION	8	chain C and resseq 43:137	C	43 - 137
9	X-RAY DIFFRACTION	9	chain C and resseq 138:249	C	138 - 249
10	X-RAY DIFFRACTION	10	chain D and resseq 1:42	D	1 - 42
11	X-RAY DIFFRACTION	11	chain D and resseq 43:137	D	43 - 137
12	X-RAY DIFFRACTION	12	chain D and resseq 138:249	D	138 - 249
13	X-RAY DIFFRACTION	13	chain E and resseq 1:42	E	1 - 42
14	X-RAY DIFFRACTION	14	chain E and resseq 43:137	E	43 - 137
15	X-RAY DIFFRACTION	15	chain E and resseq 138:249	E	138 - 249
16	X-RAY DIFFRACTION	16	chain F and resseq 1:42	F	1 - 42
17	X-RAY DIFFRACTION	17	chain F and resseq 43:137	F	43 - 137
18	X-RAY DIFFRACTION	18	chain F and resseq 138:249	F	138 - 249

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