PDB-4rwz: Crystal structure of the antibiotic-resistance methyltransferase Kmr

ID or keywords:

Entry

Database: PDB / ID: 4rwz

Title

Crystal structure of the antibiotic-resistance methyltransferase Kmr

Components

Putative rRNA methyltransferase

Keywords

TRANSFERASE / methyltransferase / RNA binding

Function / homology

S-adenosylmethionine-dependent methyltransferase activity / Vaccinia Virus protein VP39 / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative rRNA methyltransferase

Function and homology information

Biological species

Sorangium cellulosum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.801 Å

Authors

Savic, M.

Citation

Journal: Antimicrob.Agents Chemother. / Year: 2015
Title: 30S Subunit-Dependent Activation of the Sorangium cellulosum So ce56 Aminoglycoside Resistance-Conferring 16S rRNA Methyltransferase Kmr.
Authors: Savic, M. / Sunita, S. / Zelinskaya, N. / Desai, P.M. / Macmaster, R. / Vinal, K. / Conn, G.L.

History

Deposition	Dec 8, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4rwz.cif.gz	162.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4rwz.ent.gz	131.7 KB	Display	PDB format
PDBx/mmJSON format	4rwz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4rwz_validation.pdf.gz	427.2 KB	Display	wwPDB validaton report
Full document	4rwz_full_validation.pdf.gz	429.3 KB	Display
Data in XML	4rwz_validation.xml.gz	16.7 KB	Display
Data in CIF	4rwz_validation.cif.gz	23.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rw/4rwz ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rwz	HTTPS FTP

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Related structure data

Related structure data	4rx1C C: citing same article (ref.)
Similar structure data	6dxn-1 6dxn-4 6br4-1 3m0w-2 3czt-1 6ve8-d 4k85-2 6pli-1 6vil-3 6dxn-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) 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

Deposited unit

A: Putative rRNA methyltransferase

B: Putative rRNA methyltransferase

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

1

A: Putative rRNA methyltransferase

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

2

B: Putative rRNA methyltransferase

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

Unit cell

Length a, b, c (Å)	89.643, 89.643, 126.211
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Putative rRNA methyltransferase Mass: 23904.201 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sorangium cellulosum (bacteria) / Gene: kmr / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: B2L3G9, 16S rRNA (guanine1405-N7)-methyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 163 / 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: 3.06 Å³/Da / Density % sol: 59.83 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 mM HEPES buffer pH 7.5, 22% PEG MME 2000, 200 mM potassium thiocyanate, cryoprotected with 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 193 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HS / Detector: CCD / Date: Apr 22, 2010
Radiation	Monochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 54737 / Num. obs: 54737 / % possible obs: 97.5 %

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.801→37.102 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.77 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2326	2778	5.08 %	RANDOM
R_work	0.1992	-	-	-
obs	0.2009	54688	99.66 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.801→37.102 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2957	0	0	163	3120

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.017	3028
X-RAY DIFFRACTION	f_angle_d	1.647	4124
X-RAY DIFFRACTION	f_dihedral_angle_d	11.25	1108
X-RAY DIFFRACTION	f_chiral_restr	0.114	473
X-RAY DIFFRACTION	f_plane_restr	0.009	539

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 (%)
1.801-1.8315	0.3534	122	0.3079	2420	X-RAY DIFFRACTION	94
1.8315-1.8649	0.2796	147	0.2558	2548	X-RAY DIFFRACTION	99
1.8649-1.9007	0.2615	137	0.2332	2568	X-RAY DIFFRACTION	100
1.9007-1.9395	0.2815	146	0.2191	2575	X-RAY DIFFRACTION	100
1.9395-1.9817	0.2843	126	0.2203	2566	X-RAY DIFFRACTION	100
1.9817-2.0278	0.2885	147	0.2295	2562	X-RAY DIFFRACTION	100
2.0278-2.0785	0.2543	139	0.2095	2579	X-RAY DIFFRACTION	100
2.0785-2.1347	0.2375	138	0.2035	2594	X-RAY DIFFRACTION	100
2.1347-2.1975	0.2427	123	0.2081	2585	X-RAY DIFFRACTION	100
2.1975-2.2684	0.2453	146	0.2035	2577	X-RAY DIFFRACTION	100
2.2684-2.3495	0.2424	143	0.1948	2603	X-RAY DIFFRACTION	100
2.3495-2.4435	0.2394	160	0.2085	2557	X-RAY DIFFRACTION	100
2.4435-2.5547	0.2631	131	0.2187	2601	X-RAY DIFFRACTION	100
2.5547-2.6894	0.2647	138	0.2104	2599	X-RAY DIFFRACTION	100
2.6894-2.8578	0.2814	143	0.2086	2615	X-RAY DIFFRACTION	100
2.8578-3.0783	0.2364	144	0.2115	2617	X-RAY DIFFRACTION	100
3.0783-3.3879	0.2427	119	0.1981	2643	X-RAY DIFFRACTION	100
3.3879-3.8777	0.2176	134	0.1823	2649	X-RAY DIFFRACTION	100
3.8777-4.8838	0.1878	151	0.162	2667	X-RAY DIFFRACTION	100
4.8838-37.1094	0.2193	144	0.2129	2785	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	1.9765	-0.0303	0.1398	1.0757	-0.0897	1.4573	-0.0531	0.1517	-0.3925	-0.0841	0.1072	-0.0604	0.2901	0.087	-0.0454	0.132	0.0047	-0.029	0.2607	-0.0175	0.2213	-1.7654	28.8205	-20.013
2	2.0168	0.0201	0.639	1.1013	-0.3178	1.5481	-0.3183	0.3179	-0.327	-0.0384	0.125	-0.0389	0.0957	0.0469	-0.0018	0.1187	0.0164	0.0046	0.3229	-0.0145	0.1776	2.2339	29.5699	-21.9444
3	0.7901	-0.0444	-0.1378	0.1976	0.0388	0.0156	-0.1267	0.0743	-0.0509	0.0859	0.0494	0.1428	0.1197	-0.2077	-0.5857	0.0274	-0.0465	-0.0234	0.4533	0.0324	0.2295	-16.0683	35.4295	-18.4401
4	0.6261	0.016	-0.0926	0.4018	0.2478	0.158	-0.171	0.286	0.3121	0.1189	0.1089	0.1809	0.066	-0.0191	-0.033	0.0451	-0.0044	-0.094	0.5618	0.092	0.2815	-13.179	47.888	-20.5216
5	1.6284	0.3176	-1.6572	0.6966	-0.0985	2.7882	-0.1327	-0.3505	0.3844	0.1725	-0.0635	0.1966	-0.2113	0.1665	0.0982	0.3506	-0.0254	0.0077	0.4799	0.0127	0.251	-23.4051	51.3196	-15.6333
6	1.2047	1.1998	-1.0874	1.4159	-0.4299	2.9947	-0.0348	-0.6549	0.4255	0.3853	0.0588	0.328	-0.254	-0.3221	-0.2666	0.0817	0.0031	0.0431	0.698	-0.0172	0.2281	-25.8891	38.9021	-10.3828
7	2.4604	1.7181	-0.5341	4.7421	3.1099	3.7369	0.0513	-0.4017	-0.4259	0.3017	-0.1823	0.0346	0.2334	-0.0433	0.1056	0.5334	-0.166	0.0474	0.5997	-0.0775	0.2767	-13.7172	48.225	-4.1061
8	1.8364	1.2974	0.1777	3.4675	0.1599	1.3725	-0.0299	-0.2294	0.0952	0.2873	0.0461	0.1236	-0.0186	-0.2163	0.0299	0.1283	-0.006	0.0325	0.4547	-0.0518	0.1917	-18.7293	37.6376	-8.8623
9	0.8919	-0.0766	-0.2362	0.411	-0.3485	1.3862	0.0018	0.6286	0.5148	0.1541	0.0129	-0.3082	-0.5759	0.2263	0.1414	0.3089	-0.1207	-0.1637	0.3494	0.3227	0.3099	10.4943	62.3381	-25.9345
10	0.9339	-0.1156	0.144	1.3252	-0.5767	0.5582	-0.0986	0.586	0.1301	0.1547	-0.0816	0.1953	-0.2094	0.1826	-0.0953	0.1217	-0.01	-0.0903	0.2537	0.082	0.1743	3.1853	53.8337	-20.1719
11	1.5584	-0.6384	0.4909	1.4212	-0.254	1.2993	-0.2558	0.4703	0.4578	-0.0006	-0.0167	-0.0363	-0.3077	0.2612	0.0676	0.2106	-0.0382	-0.0849	0.3703	0.1037	0.3152	5.412	56.4639	-24.8547
12	0.4496	0.1071	0.1736	1.1989	-0.4426	0.2947	-0.0738	0.0411	0.336	0.5878	-0.3367	-0.3985	-0.6084	0.5347	0.0837	0.2809	-0.1521	-0.1485	0.2963	0.0892	0.2335	14.7527	51.6597	-8.8194
13	1.1098	1.0427	-0.2496	2.9545	0.0967	0.1144	-0.0728	0.0555	0.275	0.3736	-0.0057	-0.0186	-0.7875	0.5332	-0.01	0.4665	-0.0941	-0.0846	0.2106	-0.0033	0.216	8.858	51.8667	-6.2032
14	0.7556	0.6921	0.4833	0.7386	-0.0479	2.4804	-0.3599	-0.0755	0.0921	0.416	0.2083	-0.2169	-0.0518	-0.057	0.007	0.2608	0.1512	-0.0434	0.4049	-0.0103	0.1932	16.0513	37.0706	-4.2073
15	1.2865	0.6957	-0.1244	2.4482	0.0484	0.6297	-0.1828	-0.6661	0.4168	1.2512	-0.0046	0.3221	-0.8707	-0.0814	0.0971	0.8036	0.0232	-0.141	0.4427	-0.0099	0.3871	12.3192	50.6442	3.8628
16	3.7938	2.2932	1.7922	5.9342	0.4271	0.9466	-0.4955	-0.1478	0.4361	0.4112	-0.2508	0.2527	-0.9446	-0.0007	0.0803	0.6485	-0.013	-0.0316	0.2858	-0.057	0.2521	8.1571	52.53	-0.0098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:62)
2	X-RAY DIFFRACTION	2	(chain A and resid 63:92)
3	X-RAY DIFFRACTION	3	(chain A and resid 93:133)
4	X-RAY DIFFRACTION	4	(chain A and resid 134:150)
5	X-RAY DIFFRACTION	5	(chain A and resid 151:163)
6	X-RAY DIFFRACTION	6	(chain A and resid 164:181)
7	X-RAY DIFFRACTION	7	(chain A and resid 182:184)
8	X-RAY DIFFRACTION	8	(chain A and resid 206:216)
9	X-RAY DIFFRACTION	9	(chain B and resid 1:25)
10	X-RAY DIFFRACTION	10	(chain B and resid 26:66)
11	X-RAY DIFFRACTION	11	(chain B and resid 67:92)
12	X-RAY DIFFRACTION	12	(chain B and resid 93:127)
13	X-RAY DIFFRACTION	13	(chain B and resid 128:143)
14	X-RAY DIFFRACTION	14	(chain B and resid 144:161)
15	X-RAY DIFFRACTION	15	(chain B and resid 162:186)
16	X-RAY DIFFRACTION	16	(chain B and resid 206:214)

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