PDB-6k0w: DNA methyltransferase in complex with sinefungin

ID or keywords:

Entry

Database: PDB / ID: 6k0w

Title

DNA methyltransferase in complex with sinefungin

Components

Adenine specific DNA methyltransferase (Mod)

Keywords

DNA BINDING PROTEIN / DNA methyltransferase / sinefungin

Function / homology

Function and homology information

macromolecule modification / N-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) activity / methyltransferase activity / methylation / DNA binding / cytoplasm
Similarity search - Function

Biological species

Helicobacter pylori 26695 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 2.65 Å

Authors

Narayanan, N. / Nair, D.T.

Funding support

India, 1items

Citation

Journal: J.Mol.Biol. / Year: 2020
Title: Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress.
Authors: Narayanan, N. / Banerjee, A. / Jain, D. / Kulkarni, D.S. / Sharma, R. / Nirwal, S. / Rao, D.N. / Nair, D.T.

History

Deposition	May 7, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 11, 2019	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2	Mar 27, 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	6k0w.cif.gz	750.8 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	6k0w_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	6k0w_full_validation.pdf.gz	1.4 MB	Display
Data in XML	6k0w_validation.xml.gz	67.5 KB	Display
Data in CIF	6k0w_validation.cif.gz	90.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k0/6k0w ftp://data.pdbj.org/pub/pdb/validation_reports/k0/6k0w	HTTPS FTP

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Related structure data

Similar structure data	6p9y-d 5iso-1 0993 2d31-2 21992 3207 3s1s-d 20277 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) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

B: Adenine specific DNA methyltransferase (Mod)

A: Adenine specific DNA methyltransferase (Mod)

C: Adenine specific DNA methyltransferase (Mod)

D: Adenine specific DNA methyltransferase (Mod)

hetero molecules

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

1

B: Adenine specific DNA methyltransferase (Mod)

D: Adenine specific DNA methyltransferase (Mod)

hetero molecules

defined by author&software
142 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Adenine specific DNA methyltransferase (Mod)

C: Adenine specific DNA methyltransferase (Mod)

hetero molecules

defined by author&software
142 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.810, 88.480, 163.330
Angle α, β, γ (deg.)	90.00, 96.50, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein	Adenine specific DNA methyltransferase (Mod) Mass: 70619.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: HP_0593 / Plasmid: pet14b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: O25315
#2: Chemical	ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE Mass: 381.387 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.25 Å³/Da / Density % sol: 62.11 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20%PEG 5KMME,20%PEG 5KMME, 0.1M NaCl and 0.1M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2012 / Details: bent collimating mirror and toroid
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.65→50.503 Å / Num. obs: 102152 / % possible obs: 100 % / Observed criterion σ(I): 2.2 / Redundancy: 3.7 % / R_merge(I) obs: 0.074 / R_pim(I) all: 0.045 / Net I/σ(I): 10
Reflection shell	Resolution: 2.65→2.79 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14825 / R_pim(I) all: 0.339 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
iMOSFLM		data reduction
SCALA		data scaling
AutoSol		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 2.65→50.503 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.21

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2578	5089	4.98 %	0.257
R_work	0.2058	-	-	-
obs	0.2084	102152	99.87 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.65→50.503 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14259	0	108	91	14458

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	14618
X-RAY DIFFRACTION	f_angle_d	0.978	19768
X-RAY DIFFRACTION	f_dihedral_angle_d	5.308	8703
X-RAY DIFFRACTION	f_chiral_restr	0.054	2228
X-RAY DIFFRACTION	f_plane_restr	0.006	2561

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 (%)
2.65-2.6802	0.3646	162	0.3192	3243	X-RAY DIFFRACTION	100
2.6802-2.7117	0.3706	168	0.2984	3207	X-RAY DIFFRACTION	100
2.7117-2.7447	0.3275	156	0.2568	3188	X-RAY DIFFRACTION	100
2.7447-2.7795	0.2604	154	0.2488	3262	X-RAY DIFFRACTION	100
2.7795-2.8161	0.3024	170	0.2335	3220	X-RAY DIFFRACTION	100
2.8161-2.8546	0.272	178	0.2355	3187	X-RAY DIFFRACTION	100
2.8546-2.8954	0.2822	142	0.238	3204	X-RAY DIFFRACTION	100
2.8954-2.9386	0.2901	157	0.2388	3249	X-RAY DIFFRACTION	100
2.9386-2.9845	0.3036	165	0.2306	3214	X-RAY DIFFRACTION	100
2.9845-3.0335	0.2879	152	0.234	3264	X-RAY DIFFRACTION	100
3.0335-3.0858	0.2838	167	0.2374	3214	X-RAY DIFFRACTION	100
3.0858-3.1419	0.3023	155	0.2389	3213	X-RAY DIFFRACTION	100
3.1419-3.2023	0.2742	173	0.2248	3220	X-RAY DIFFRACTION	100
3.2023-3.2676	0.2519	176	0.2134	3243	X-RAY DIFFRACTION	100
3.2676-3.3387	0.2497	171	0.2039	3194	X-RAY DIFFRACTION	100
3.3387-3.4163	0.2537	194	0.1879	3226	X-RAY DIFFRACTION	100
3.4163-3.5017	0.2495	203	0.1939	3165	X-RAY DIFFRACTION	100
3.5017-3.5964	0.2449	172	0.1868	3244	X-RAY DIFFRACTION	100
3.5964-3.7022	0.2679	177	0.1976	3254	X-RAY DIFFRACTION	100
3.7022-3.8216	0.2192	164	0.1904	3218	X-RAY DIFFRACTION	100
3.8216-3.9582	0.266	164	0.1916	3225	X-RAY DIFFRACTION	100
3.9582-4.1166	0.2535	168	0.1858	3249	X-RAY DIFFRACTION	100
4.1166-4.3039	0.1883	184	0.1694	3225	X-RAY DIFFRACTION	100
4.3039-4.5306	0.2026	170	0.1631	3249	X-RAY DIFFRACTION	100
4.5306-4.8143	0.2288	187	0.1725	3226	X-RAY DIFFRACTION	100
4.8143-5.1857	0.2594	196	0.198	3249	X-RAY DIFFRACTION	100
5.1857-5.7069	0.2926	173	0.2087	3231	X-RAY DIFFRACTION	100
5.7069-6.5312	0.2951	143	0.2341	3324	X-RAY DIFFRACTION	100
6.5312-8.2228	0.2646	167	0.2168	3305	X-RAY DIFFRACTION	100
8.2228-50.503	0.2661	181	0.2167	3351	X-RAY DIFFRACTION	99

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	1.9527	2.1611	-1.0567	3.9515	-2.9347	2.5427	0.0036	0.8759	-0.2182	0.2092	0.5192	-0.4129	0.9672	-0.2087	-0.1595	0.9103	-0.0843	-0.0208	0.4531	-0.0838	0.49	144.3079	44.0772	363.4949
2	5.1628	1.8304	-0.0006	4.0283	0.4038	3.0553	-0.096	0.4038	0.0947	-0.4013	0.2393	0.2019	0.6367	-0.033	-0.0622	0.9378	-0.0986	-0.2023	0.3255	-0.0309	0.3372	134.8747	33.3486	380.1267
3	1.8315	0.0213	-0.4481	2.3399	0.5013	3.023	0.0702	0.2705	0.0901	-0.0791	0.189	-0.1249	0.418	0.0334	-0.2907	0.6809	-0.0126	-0.0711	0.2938	0.0289	0.4001	141.7535	46.0686	377.8216
4	3.4232	3.2213	-2.7555	6.8573	-3.3072	7.0417	-0.2264	0.2485	-1.9147	0.346	0.6603	-1.3878	-0.5694	-1.3018	-0.2348	1.4284	-0.2082	-0.2509	0.8877	0.0594	1.4571	116.4886	38.6429	410.0047
5	2.1624	-0.3423	0.7421	3.4623	1.6602	3.2745	0.05	-0.3188	-0.1814	0.7254	0.2522	0.074	0.7654	-0.2309	-0.2411	0.9785	-0.1094	-0.1062	0.3614	0.06	0.4898	134.713	40.5567	395.2884
6	5.0274	-1.5753	-0.9584	2.8056	0.0183	2.84	0.074	-0.2597	-0.2299	0.2901	0.2493	-0.2455	0.9568	0.1851	-0.2158	1.2428	-0.1238	-0.3281	0.3641	0.01	0.5253	139.1198	25.8257	390.9043
7	2.7137	1.0243	1.7976	4.3916	3.1692	3.6618	0.2953	0.0437	-0.502	0.1674	-0.3827	0.5439	1.4333	-1.3926	0.2127	1.4999	-0.4822	-0.3635	0.8572	0.0294	0.7577	119.5072	17.1214	370.475
8	2.8367	0.6218	-0.6483	2.1265	-0.1937	1.8607	-0.1351	-0.6125	-0.5909	0.3407	0.1313	1.1609	0.5541	-0.4393	0.0692	0.4926	-0.1342	0.2453	0.587	-0.123	1.0355	181.8191	73.7848	336.3485
9	1.9954	0.1972	-0.3221	2.4762	-0.7452	1.5622	-0.0781	-0.0231	-0.1069	0.0455	-0.0287	0.7753	0.1376	-0.4799	0.1169	0.2905	-0.0281	0.0671	0.4032	-0.1312	0.7364	183.3681	86.2636	330.0883
10	6.0244	-1.3512	-1.4235	2.7276	0.3242	6.3046	-0.0847	-1.5069	-0.4333	0.8914	-0.0617	-0.8009	0.7024	0.535	0.1167	1.35	-0.122	-0.2894	0.9601	0.12	1.008	219.7032	82.7384	350.1419
11	3.3022	0.5891	-1.7115	6.8252	-0.3642	1.5509	-0.1142	0.0243	-0.2537	-0.1261	0.0219	-0.3319	0.1075	0.1962	0.0091	0.3058	-0.0082	-0.0153	0.2827	0.0013	0.4867	202.6032	84.6378	329.3788
12	4.295	0.9839	1.4885	5.5699	2.6405	6.5436	0.0243	0.1527	-0.5924	-0.0171	-0.1697	-0.009	0.5211	0.0914	0.2221	0.3344	-0.0429	0.1592	0.2587	0.0529	0.6239	195.853	70.2968	330.5795
13	5.2034	3.86	-4.2421	4.0145	-3.3118	5.9782	0.1236	-0.8836	-1.1145	0.8413	-0.4583	0.2708	-0.1702	-0.1369	0.1543	0.7896	-0.073	0.389	0.6064	0.1439	1.1599	181.3882	59.255	350.7222
14	1.9749	-0.2773	0.3403	2.8556	0.0829	1.2553	-0.5195	0.4381	0.3481	-0.2563	0.268	1.0436	-0.6316	-0.5095	0.1481	0.4648	0.2169	-0.2956	0.537	-0.13	1.2552	179.7491	123.2561	317.3947
15	3.6408	-0.5639	-0.7924	2.6143	-0.1306	2.2786	-0.2036	-0.4248	0.5309	0.1696	0.1422	0.8119	-0.3961	-0.652	0.1045	0.4807	0.1594	-0.1537	0.5709	-0.1774	1.0149	175.5555	117.7046	324.8637
16	1.769	-0.9109	-0.0034	3.5339	-0.1126	1.8859	-0.0319	0.0337	0.2905	-0.1282	-0.142	0.7094	-0.1345	-0.2958	0.1474	0.3458	-0.0044	-0.1099	0.311	-0.1048	0.6938	186.9106	106.1914	320.9111
17	4.2019	-0.7914	0.9025	3.3876	3.4936	4.5884	-0.176	0.0383	0.5315	0.1466	-0.078	-0.1369	-0.4378	0.0444	0.2189	0.5337	-0.0047	-0.1513	0.3257	0.0166	0.5858	202.2055	113.7939	323.3345
18	3.5993	-0.478	-0.3454	5.4627	1.5824	3.8855	-0.0911	-0.162	0.6708	-0.0349	-0.0052	-0.0411	-0.4516	0.0634	0.0762	0.477	0.0469	-0.2012	0.3002	0.0038	0.7003	195.8624	125.4558	319.9329
19	4.6683	-3.8528	3.5992	5.472	-3.0146	5.1716	0.1539	0.7345	1.0332	-0.8962	-0.6032	0.2323	-0.4188	-0.1806	0.3225	0.9729	0.2055	-0.4014	0.654	0.0659	1.1598	179.2974	138.1951	301.6284
20	3.9526	-0.1405	0.5434	2.0977	-0.7035	2.3803	0.0295	0.3387	-0.5252	-0.5048	0.5569	0.2755	-0.3851	0.3708	-0.4976	0.738	-0.1013	0.0956	0.5836	0.0481	0.5646	148.6292	58.2986	359.8756
21	3.7833	-1.6604	-3.5351	7.2279	1.1484	3.27	0.4175	-0.3303	0.2648	-0.2873	0.1037	-0.4687	-2.0538	0.7628	-0.4555	1.3074	-0.3649	0.2093	0.6048	-0.1374	1.028	157.2224	91.1763	385.4476
22	1.2998	1.9374	1.0585	5.6012	0.1826	5.325	-0.097	0.5319	0.4669	-0.5148	0.4157	-0.3376	-0.7242	0.1442	-0.2143	0.6413	-0.0928	0.2357	0.3297	-0.0063	0.5841	150.8615	76.472	379.6822
23	1.3263	3.0241	-2.1144	7.4569	-4.096	8.0335	-0.391	-0.1142	0.063	-1.3531	0.3022	1.0692	-0.7149	-1.0304	-0.2676	1.274	-0.0612	-0.0361	0.5702	0.1785	0.5626	142.8916	75.3261	360.3864
24	0.835	1.3257	-0.7273	2.5776	-0.781	2.9135	0.1556	0.1659	0.1068	-0.2572	0.1805	-0.149	-0.361	0.0415	-0.3861	0.71	-0.0475	0.0606	0.3169	-0.0265	0.5244	146.4592	64.066	382.369
25	3.1442	0.6949	-3.9237	4.8254	-1.0841	6.0235	0.2262	-0.6514	-0.2964	0.6302	0.1293	-1.2726	-0.2779	0.9046	-0.3586	0.552	-0.0776	-0.1073	0.3946	-0.1352	0.5744	156.484	61.6037	392.2316
26	5.363	-3.2563	-0.8351	5.3137	-0.1747	3.8259	0.2068	-0.1073	0.1789	0.9483	0.1766	0.568	-0.5737	-0.252	-0.327	0.8831	-0.0591	0.16	0.3342	0.0183	0.756	141.8317	73.4225	397.2111
27	2.6192	-1.0268	-0.3459	4.3639	-0.7683	3.803	0.0779	-0.2423	0.1732	0.2891	0.0779	-0.1782	-0.7114	0.2294	-0.1127	0.8646	-0.1864	0.1188	0.3335	-0.0714	0.6441	150.9987	80.3073	391.3257
28	3.5827	-1.957	0.8327	5.1215	-2.7135	1.4681	-0.0244	-0.21	0.9644	0.1903	0.2289	-0.0678	-1.7194	-0.4335	-0.0396	1.3217	-0.0195	0.2605	0.4206	0.0524	0.9238	141.6666	91.2789	392.0945
29	4.16	-1.4124	0.3927	5.565	-0.5754	0.4429	-0.3825	0.0672	0.6623	0.3134	-0.5125	-0.6362	-1.5264	0.7049	0.8894	1.2028	-0.2722	0.1889	0.5028	-0.0266	1.0411	156.4012	91.5948	387.2291
30	2.1667	0.2168	-0.0235	6.6271	-2.935	1.6162	-0.1264	0.3672	1.0318	0.23	-0.1727	-0.9181	-0.5759	0.3007	0.7006	1.9158	-1.2975	0.7491	0.4456	-0.0387	1.675	168.3628	93.6953	380.8175
31	1.3495	-0.608	0.6159	5.5983	2.8871	2.1642	0.8928	-0.1705	1.1662	0.6571	0.0974	-2.0793	-1.3092	0.7652	-0.3222	1.4174	-1.1396	0.2387	1.469	0.5114	2.1835	178.188	99.7272	376.5096

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 15 through 64 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 65 through 114 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 115 through 249 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 262 through 305 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 306 through 410 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 411 through 477 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 478 through 594 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 35 through 76 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 77 through 249 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 250 through 341 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 342 through 393 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 394 through 477 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 478 through 594 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 35 through 82 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 83 through 159 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 160 through 249 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 250 through 382 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 383 through 477 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 478 through 594 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 17 through 51 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 52 through 76 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 77 through 117 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 118 through 159 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 160 through 231 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 232 through 352 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 353 through 393 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 394 through 443 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 444 through 477 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 478 through 514 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 515 through 550 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 551 through 574 )

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