PDB-4rx1: Crystal Structure of antibiotic-resistance methyltransferase Kmr

ID or keywords:

Entry

Database: PDB / ID: 4rx1

Title

Crystal Structure of antibiotic-resistance methyltransferase Kmr

Components

Putative rRNA methyltransferase

Keywords

TRANSFERASE / RNA methyltransferase / methyltransferase / ribosomal RNA

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 / IODIDE ION / Putative rRNA methyltransferase

Function and homology information

Biological species

Sorangium cellulosum (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 2.472 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 / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rx1.cif.gz	170.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4rx1.ent.gz	138.3 KB	Display	PDB format
PDBx/mmJSON format	4rx1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rx1_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	4rx1_full_validation.pdf.gz	457.1 KB	Display
Data in XML	4rx1_validation.xml.gz	19.1 KB	Display
Data in CIF	4rx1_validation.cif.gz	26.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rx/4rx1 ftp://data.pdbj.org/pub/pdb/validation_reports/rx/4rx1	HTTPS FTP

-
Related structure data

Related structure data	4rwzC C: citing same article (ref.)
Similar structure data	1bkc-1 6ta7-2 2i47-2 3rq4-d 1bkc-4 2i47-3 6onb-1 3g42-4 1zxc-1 4h8n-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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative rRNA methyltransferase

B: Putative rRNA methyltransferase

hetero molecules

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

1

A: Putative rRNA methyltransferase

hetero molecules

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

2

B: Putative rRNA methyltransferase

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	89.506, 89.506, 127.875
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): BL21(DE3) References: UniProt: B2L3G9, 16S rRNA (guanine1405-N7)-methyltransferase
#2: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 3.09 Å³/Da / Density % sol: 60.23 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 100 mM MES buffer pH 6.1, 6% PEG MME 5000, 8% 1-propanol, 0.5 mM SAM, 100 mM sodium iodide, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction	Mean temperature: 193 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
Detector	Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 11, 2011
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 2.47→50 Å / Num. all: 21690 / Num. obs: 21690 / % possible obs: 99.1 %

-
Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.472→37.35 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 26.19 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2631	1105	5.11 %	RANDOM
R_work	0.2137	-	-	-
obs	0.2162	21619	99.4 %	-
all	-	21619	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.472→37.35 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3133	0	11	153	3297

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	3201
X-RAY DIFFRACTION	f_angle_d	1.397	4351
X-RAY DIFFRACTION	f_dihedral_angle_d	13.237	1170
X-RAY DIFFRACTION	f_chiral_restr	0.079	494
X-RAY DIFFRACTION	f_plane_restr	0.007	567

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 (%)
2.472-2.5847	0.3739	153	0.2443	2427	X-RAY DIFFRACTION	97
2.5847-2.7209	0.2725	136	0.2256	2549	X-RAY DIFFRACTION	100
2.7209-2.8913	0.291	127	0.2292	2546	X-RAY DIFFRACTION	100
2.8913-3.1145	0.2549	151	0.2252	2517	X-RAY DIFFRACTION	100
3.1145-3.4277	0.263	149	0.2076	2541	X-RAY DIFFRACTION	100
3.4277-3.9232	0.2474	137	0.1938	2582	X-RAY DIFFRACTION	100
3.9232-4.9411	0.2296	132	0.1817	2604	X-RAY DIFFRACTION	100
4.9411-37.3546	0.2744	120	0.2471	2748	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	0.5615	0.1548	-0.1786	1.0271	-0.0255	0.9879	0.1092	-0.0482	0.2583	-0.037	-0.1351	0.3265	-0.042	-0.2969	0.0104	0.1331	-0.0293	0.0298	0.1471	-0.0298	0.2048	25.796	-13.7358	0.1421
2	0.013	-0.0177	-0.1075	0.0245	0.1478	0.857	0.0002	-0.0168	0.016	0.0456	-0.0208	0.0062	0.0269	-0.0058	-0.0363	0.0714	-0.1393	0.0414	0.1371	-0.0525	0.0076	17.5304	-23.8205	5.0003
3	1.8509	1.1521	-0.9851	2.15	-0.9086	1.8867	0.0319	0.0402	0.0797	-0.1382	-0.0166	0.0395	-0.1063	-0.0654	-0.0211	0.1413	-0.0395	0.0426	0.1058	-0.0641	0.1599	29.8474	-8.306	-3.6557
4	0.2801	-0.0785	0.001	0.458	0.0457	0.1365	-0.0245	-0.0803	0.1076	0.1209	-0.071	0.1332	-0.127	-0.0107	0.0362	0.2193	-0.0552	0.0174	0.0708	-0.0323	0.1767	40.4785	-4.5336	1.7406
5	0.904	-0.5237	-0.3251	1.454	0.5732	1.1315	0.0326	-0.0591	0.149	0.0792	-0.16	-0.0942	0.0518	0.1093	0.0512	0.2069	-0.0569	0.0537	0.146	0.058	0.2695	46.1638	-7.4511	1.9858
6	1.4406	0.2013	0.3772	0.6878	0.5294	0.6799	0.0354	-0.1351	-0.0414	0.1768	-0.0977	-0.02	0.0815	-0.0549	-0.1135	0.3161	-0.1992	0.0009	0.2139	-0.0719	0.2179	48.6376	0.0766	12.0549
7	0.2647	0.1316	-0.3528	0.0759	-0.1648	0.4806	0.0303	-0.264	-0.3408	0.1744	-0.0304	-0.2214	0.4052	0.2377	0.024	1.1889	0.0616	-0.0545	1.0024	-0.0315	0.9288	49.5698	-23.7901	15.8912
8	0.2449	0.078	-0.0867	0.0678	-0.1113	0.1915	0.037	-0.0708	0.0357	0.0403	-0.0084	0.034	-0.0556	0.0142	0.0563	0.0553	-0.0827	0.0469	0.0485	-0.0181	-0.0192	42.3901	-2.2034	11.8694
9	0.632	0.0104	-0.0594	0.2327	0.1719	0.4743	-0.2376	0.0026	-0.1633	-0.0257	-0.0421	-0.0742	0.2121	0.2706	-0.3136	0.2344	0.0361	0.1831	0.1772	0.0664	0.1711	47.0013	-32.5405	-1.1473
10	1.2984	0.0955	-0.0039	0.72	0.0104	0.6661	-0.2103	0.0246	-0.2688	0.0441	-0.1114	0.0159	0.2071	0.0923	0.0563	0.225	-0.0026	0.1253	0.1794	0.0512	0.1681	46.3483	-33.5426	-1.4668
11	0.1647	-0.3132	-0.1609	0.6186	0.2291	0.5219	-0.1485	-0.005	-0.2266	0.0195	-0.1405	-0.032	0.2831	0.174	-0.1594	0.2284	0.0528	0.0941	0.1659	0.0631	0.1381	37.9377	-35.2477	12.1088
12	0.515	0.0601	0.1627	1.2596	-0.7559	1.011	0.0306	-0.0195	-0.0697	0.0018	-0.0515	-0.0424	0.1238	0.0414	0.032	0.5629	0.1152	0.2213	0.3071	0.202	0.3905	42.0359	-42.1998	15.1625
13	0.3271	0.1344	0.0254	0.5762	-0.1206	0.332	-0.0585	-0.0241	-0.0409	-0.0334	-0.0234	0.052	0.1166	-0.1314	-0.0539	0.1737	-0.1349	0.0572	0.2547	-0.0049	0.155	27.4941	-30.1693	12.5096
14	0.1257	-0.0952	0.0243	0.2999	0.1762	0.1769	-0.1448	-0.071	-0.1097	0.0883	-0.1093	-0.0427	0.3162	0.2098	-0.1279	0.2504	-0.0525	0.0987	0.3325	0.0807	0.1324	33.5349	-36.1595	25.5566
15	4.0266	-0.5567	2.8269	2.283	-0.6487	3.6924	-0.2448	0.1801	0.2843	-0.1444	0.0695	0.0992	-0.3291	-0.1414	0.2189	0.2063	-0.0537	-0.0857	0.2978	-0.0223	0.1534	36.173	-23.0222	22.6941
16	0.239	-0.3184	-0.1903	1.5377	-0.1418	0.342	-0.0688	-0.1155	-0.026	-0.0277	-0.0289	-0.1143	0.1882	0.213	-0.0395	0.4358	0.2809	-0.0094	0.4332	0.0111	0.1661	44.1945	-34.9319	21.7205

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 1:70)
2	X-RAY DIFFRACTION	2	(chain A and resid 71:77)
3	X-RAY DIFFRACTION	3	(chain A and resid 78:92)
4	X-RAY DIFFRACTION	4	(chain A and resid 93:125)
5	X-RAY DIFFRACTION	5	(chain A and resid 126:157)
6	X-RAY DIFFRACTION	6	(chain A and resid 158:186)
7	X-RAY DIFFRACTION	7	(chain A and resid 191:204)
8	X-RAY DIFFRACTION	8	(chain A and resid 205:217)
9	X-RAY DIFFRACTION	9	(chain B and resid 1:70)
10	X-RAY DIFFRACTION	10	(chain B and resid 71:92)
11	X-RAY DIFFRACTION	11	(chain B and resid 93:117)
12	X-RAY DIFFRACTION	12	(chain B and resid 118:134)
13	X-RAY DIFFRACTION	13	(chain B and resid 135:151)
14	X-RAY DIFFRACTION	14	(chain B and resid 152:178)
15	X-RAY DIFFRACTION	15	(chain B and resid 179:207)
16	X-RAY DIFFRACTION	16	(chain B and resid 208:214)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi