PDB-6cn0: 2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteu...

ID or keywords:

Entry

Database: PDB / ID: 6cn0

Title

2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteus mirabilis

Components

16S rRNA (guanine(1405)-N(7))-methyltransferase

Keywords

TRANSFERASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

16S rRNA (guanine1405-N7)-methyltransferase / Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria / Ribosomal RNA aminoglycoside-resistance methyltransferase / Ribosomal RNA methyltransferase (FmrO) / rRNA methyltransferase activity / S-adenosyl-L-methionine-dependent methyltransferase superfamily / response to antibiotic /

CITRIC ACID / 16S rRNA (guanine(1405)-N(7))-methyltransferase

Function and homology information

Biological species

Proteus mirabilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

Minasov, G. / Wawrzak, Z. / Di Leo, R. / Evdokimova, E. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.95 Angstrom Crystal Structure of 16S rRNA Methylase from Proteus mirabilis.
Authors: Minasov, G. / Wawrzak, Z. / Di Leo, R. / Evdokimova, E. / Savchenko, A. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Mar 6, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	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	6cn0.cif.gz	442.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6cn0.ent.gz	369.8 KB	Display	PDB format
PDBx/mmJSON format	6cn0.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cn/6cn0 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/6cn0	HTTPS FTP

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Related structure data

Related structure data	3lcuS S: Starting model for refinement
Similar structure data	6pqb-2 1u0j-d 4uu9-1 1wm0-d 1g5s-d 5lnb-d 3ewn-d 2aeg-1 5nqx-2 4fks-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) 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
Other databases	TargetTrack: CSGID-IDP91051

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (4)

Deposited unit

A: 16S rRNA (guanine(1405)-N(7))-methyltransferase

B: 16S rRNA (guanine(1405)-N(7))-methyltransferase

C: 16S rRNA (guanine(1405)-N(7))-methyltransferase

D: 16S rRNA (guanine(1405)-N(7))-methyltransferase

hetero molecules

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

1

A: 16S rRNA (guanine(1405)-N(7))-methyltransferase

hetero molecules

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

2

B: 16S rRNA (guanine(1405)-N(7))-methyltransferase

hetero molecules

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

3

C: 16S rRNA (guanine(1405)-N(7))-methyltransferase

hetero molecules

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

4

D: 16S rRNA (guanine(1405)-N(7))-methyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	158.318, 158.318, 122.892
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	16S rRNA (guanine(1405)-N(7))-methyltransferase / 16S rRNA m7G1405 methyltransferase Mass: 32419.094 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: rmtC / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q33DX5, 16S rRNA (guanine1405-N7)-methyltransferase
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.48 Å³/Da / Density % sol: 64.7 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Protein: 10.0 mg/ml, 0.3M Sodium chloride, 2mM Magnesium chloride, 0.01M HEPES (pH 7.5), Screen: 2M Ammonium Sulfate, 0.1M Sodium citrate (pH 5.6), 1% Isopropanol, Cryo: paratone

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2016 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.95→30 Å / Num. obs: 36800 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / B_iso Wilson estimate: 95.8 Å² / R_merge(I) obs: 0.053 / R_pim(I) all: 0.027 / R_rim(I) all: 0.06 / R_sym value: 0.053 / Χ²: 1.004 / Net I/σ(I): 25.7
Reflection shell	Resolution: 2.95→3 Å / Redundancy: 4.7 % / R_merge(I) obs: 0.874 / Mean I/σ(I) obs: 2 / Num. unique obs: 1815 / CC_1/2: 0.612 / R_pim(I) all: 0.446 / R_rim(I) all: 0.986 / R_sym value: 0.874 / Χ²: 1.014 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0189	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LCU

3lcu

Resolution: 2.95→29.98 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.921 / SU B: 39.692 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R: 2.833 / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26286	1865	5.1 %	RANDOM
R_work	0.21789	-	-	-
obs	0.22014	34904	99.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 113.934 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0.12 Å²	0 Å²
2-	-	0.25 Å²	0 Å²
3-	-	-	-0.8 Å²

Refinement step

Cycle: 1 / Resolution: 2.95→29.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8544	0	44	23	8611

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	8738
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8319
X-RAY DIFFRACTION	r_angle_refined_deg	1.298	1.988	11783
X-RAY DIFFRACTION	r_angle_other_deg	0.881	3	19348
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.773	5	1047
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	19.831	24.506	395
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.822	15	1653
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.808	15	49
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	1325
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.021	9430
X-RAY DIFFRACTION	r_gen_planes_other	0.02	0.02	1707
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	2.28	6.788	4221
X-RAY DIFFRACTION	r_mcbond_other	2.279	6.787	4220
X-RAY DIFFRACTION	r_mcangle_it	3.9	10.176	5257
X-RAY DIFFRACTION	r_mcangle_other	3.9	10.177	5258
X-RAY DIFFRACTION	r_scbond_it	2.133	7.054	4517
X-RAY DIFFRACTION	r_scbond_other	2.131	7.052	4515
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.65	10.497	6526
X-RAY DIFFRACTION	r_long_range_B_refined	7.203	80.48	9997
X-RAY DIFFRACTION	r_long_range_B_other	7.202	80.488	9998
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.952→3.027 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.358	130	-
R_work	0.314	2521	-
obs	-	-	99.92 %

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	0.9899	-1.4596	-0.4466	7.9744	1.2315	10.1045	0.2439	-0.2624	0.5203	0.5941	0.0914	-0.2356	-0.771	0.7033	-0.3353	0.4118	-0.0189	0.0445	0.3406	-0.3534	0.5561	51.8512	37.683	33.022
2	1.8157	-2.9295	-2.698	5.0819	3.1481	9.9954	-0.0372	0.2053	0.2215	0.0401	-0.318	-0.5189	0.0376	0.5506	0.3552	0.0638	-0.0229	0.0467	0.4854	0.01	0.458	63.5479	17.6905	4.213
3	4.6612	-0.3303	0.2616	4.0479	-1.0035	4.4608	0.1001	0.0102	0.3048	0.1037	-0.1086	-0.4182	0.0452	0.0632	0.0085	0.1582	0.1502	-0.1368	0.1561	-0.1208	0.1742	56.1525	14.6408	17.2991
4	6.4634	-0.0427	0.6473	7.1992	0.6374	3.7033	-0.1578	-1.158	0.2069	0.8523	0.0827	-0.3951	-0.0185	-0.0087	0.0751	0.3287	0.1914	-0.1942	0.334	-0.1379	0.1192	59.4688	12.403	33.7384
5	7.685	1.8889	-2.524	5.1404	3.9533	10.4832	-0.0061	-0.3104	0.319	-0.5754	-0.281	-0.0973	-0.802	0.5724	0.2872	0.4162	0.0796	-0.0284	0.1299	0.0557	0.3361	45.0592	40.0543	-1.6347
6	6.9062	1.7915	1.236	4.6413	0.0426	0.33	-0.2972	0.6226	0.0824	-0.4349	0.1424	-0.6681	-0.1359	0.2656	0.1548	0.668	0.1426	0.1524	0.8598	-0.0442	0.5396	61.7264	19.8104	-25.5283
7	5.1733	0.6428	-0.2476	4.1235	1.1732	6.2354	0.0099	0.8964	0.4034	-0.3593	0.2208	-0.3503	-0.3512	0.5043	-0.2307	0.4689	0.2302	-0.0058	0.3706	-0.0068	0.1733	45.247	21.1055	-19.8435
8	4.6091	0.141	2.0397	1.9492	-0.153	7.2648	0.5419	-0.1097	-0.0977	-0.3716	-0.1647	-0.1773	0.2313	0.1121	-0.3772	0.3907	0.1622	-0.1652	0.1025	-0.1019	0.1845	42.4027	8.1519	-8.3157
9	7.3991	-0.0359	-0.4988	12.1066	-8.5722	7.9521	-0.1345	0.2551	0.4626	0.299	0.2491	-0.1446	-0.6011	0.8826	-0.1146	0.4954	-0.1567	0.2879	0.6707	-0.0177	0.2747	99.006	12.0247	-27.0991
10	1.0673	0.037	2.3145	0.1619	0.2028	5.214	-0.3315	-0.3684	0.0184	0.2742	0.3734	-0.2092	-0.838	-0.2379	-0.0418	2.1871	0.2925	0.3249	1.9058	0.0926	1.385	88.1497	0.6336	-2.6286
11	3.7299	-0.3874	1.5602	1.8491	0.357	5.0753	0.0773	-0.7873	-0.2245	0.5443	-0.2686	0.3647	1.1336	0.5926	0.1913	0.8825	0.1066	0.5881	0.5546	0.0573	0.4909	82.486	-5.6646	-11.9609
12	3.7706	-3.5407	1.7309	3.5495	-0.3942	7.6319	-0.0303	0.6263	-0.4797	0.0048	-0.7869	0.6629	-0.3339	-0.6939	0.8172	0.4651	-0.1035	0.4169	0.5278	-0.2724	0.7351	71.5102	7.3804	-18.2441
13	7.0061	1.3935	-1.8724	7.1249	2.6166	9.0991	0.1155	0.5167	-0.4375	-0.437	-0.3156	0.443	0.5958	-0.3481	0.2001	0.183	0.176	-0.1459	0.4495	-0.3123	0.2389	17.3069	22.4393	-1.3427
14	4.8953	1.1693	-2.2858	4.0458	-0.3503	8.797	-0.1409	-0.5937	-1.5772	0.4112	0.1101	0.1042	1.0338	-0.6666	0.0307	0.7756	0.0208	-0.0235	0.4965	0.0784	0.8332	13.3567	19.8417	32.0806
15	2.9173	0.3116	-1.0324	2.7726	-0.3806	4.343	0.1038	0.3825	-0.1581	0.4474	0.0466	0.2363	0.451	-0.085	-0.1504	0.1733	0.0838	-0.0176	0.3846	-0.2252	0.169	19.777	31.1127	26.5087
16	3.7788	-1.9375	0.1655	4.2586	1.5421	3.3178	0.1304	0.0157	0.0533	0.0557	-0.1186	-0.0004	0.5217	-0.2668	-0.0119	0.1491	0.078	-0.074	0.2919	-0.1748	0.1286	35.1783	25.55	19.0634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 65
2	X-RAY DIFFRACTION	2	A	66 - 104
3	X-RAY DIFFRACTION	3	A	105 - 193
4	X-RAY DIFFRACTION	4	A	194 - 281
5	X-RAY DIFFRACTION	5	B	1 - 64
6	X-RAY DIFFRACTION	6	B	65 - 115
7	X-RAY DIFFRACTION	7	B	116 - 236
8	X-RAY DIFFRACTION	8	B	237 - 281
9	X-RAY DIFFRACTION	9	C	5 - 49
10	X-RAY DIFFRACTION	10	C	50 - 115
11	X-RAY DIFFRACTION	11	C	116 - 209
12	X-RAY DIFFRACTION	12	C	210 - 281
13	X-RAY DIFFRACTION	13	D	5 - 60
14	X-RAY DIFFRACTION	14	D	63 - 113
15	X-RAY DIFFRACTION	15	D	114 - 193
16	X-RAY DIFFRACTION	16	D	194 - 281

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