PDB-4onj: Crystal structure of the catalytic domain of ntDRM

ID or keywords:

Entry

Database: PDB / ID: 4onj

Title

Crystal structure of the catalytic domain of ntDRM

Components

DNA methyltransferase

Keywords

TRANSFERASE/TRANSFERASE INHIBITOR /

DNA methyltransferase / TRANSFERASE-TRANSFERASE INHIBITOR complex

Function / homology

Function and homology information

S-adenosylmethionine-dependent methyltransferase activity / :
Similarity search - Function

Biological species

Nicotiana tabacum (common tobacco)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.807 Å

Authors

Du, J. / Patel, D.J.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2014
Title: Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases.
Authors: Zhong, X. / Du, J. / Hale, C.J. / Gallego-Bartolome, J. / Feng, S. / Vashisht, A.A. / Chory, J. / Wohlschlegel, J.A. / Patel, D.J. / Jacobsen, S.E.

History

Deposition	Jan 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 4, 2014	Provider: repository / Type: Initial release
Revision 1.1	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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4onj.cif.gz	282.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4onj.ent.gz	231.8 KB	Display	PDB format
PDBx/mmJSON format	4onj.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/4onj ftp://data.pdbj.org/pub/pdb/validation_reports/on/4onj	HTTPS FTP

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Related structure data

Related structure data	4onqC C: citing same article (ref.)
Similar structure data	3mbo-3 6wjc-d 5yh3-1 2isg-d 6uvv-d 7c0l-d 5d79-d 1jmo-d 1f4t-d 4x7i-d 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 (4) #226 - Oct 2018 Aminoglycoside Antibiotics and Resistance similarity (1)

Deposited unit

A: DNA methyltransferase

B: DNA methyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	153.324, 153.324, 148.967
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	DNA methyltransferase / / ntDRM Mass: 40508.254 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 255-608) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Gene: DRM, NtDRM1 / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL References: UniProt: Q76KU6, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅

#1: Protein

DNA methyltransferase /

/ ntDRM

Mass: 40508.254 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 255-608)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Nicotiana tabacum (common tobacco) / Gene: DRM, NtDRM1 / Plasmid: pET-SUMO / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q76KU6,

Transferases; Transferring one-carbon groups; Methyltransferases

#2: Chemical

ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE

Mass: 381.387 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₃N₇O₅

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 6.24 Å³/Da / Density % sol: 80.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.19 M calcium chloride, 5% glycerol, 26.6% PEG400, 0.095 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2012
Radiation	Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.8→50 Å / Num. all: 52067 / Num. obs: 52015 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / B_iso Wilson estimate: 60.66 Å² / R_merge(I) obs: 0.122 / R_sym value: 0.122 / Net I/σ(I): 24.2
Reflection shell	Resolution: 2.8→2.9 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.723 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4886 / R_sym value: 0.723 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.807→46.51 Å / SU ML: 0.34 / σ(F): 1.37 / Phase error: 23.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2207	2508	5.07 %	RANDOM
R_work	0.2006	-	-	-
obs	0.2016	49507	99.39 %	-
all	-	52015	-	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.168 Å² / k_sol: 0.333 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-10.3208 Å²	0 Å²	0 Å²
2-	-	-10.3208 Å²	0 Å²
3-	-	-	20.6417 Å²

Refinement step

Cycle: LAST / Resolution: 2.807→46.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5332	0	54	0	5386

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5535
X-RAY DIFFRACTION	f_angle_d	1.288	7523
X-RAY DIFFRACTION	f_dihedral_angle_d	14.857	2069
X-RAY DIFFRACTION	f_chiral_restr	0.191	809
X-RAY DIFFRACTION	f_plane_restr	0.005	972

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 (%)
2.807-2.8611	0.3623	143	0.3074	2377	X-RAY DIFFRACTION	92
2.8611-2.9195	0.2993	144	0.2804	2568	X-RAY DIFFRACTION	100
2.9195-2.9829	0.3021	146	0.2545	2591	X-RAY DIFFRACTION	100
2.9829-3.0523	0.2711	122	0.2412	2616	X-RAY DIFFRACTION	100
3.0523-3.1286	0.2918	127	0.2454	2637	X-RAY DIFFRACTION	100
3.1286-3.2132	0.289	160	0.2295	2534	X-RAY DIFFRACTION	100
3.2132-3.3077	0.2589	154	0.2228	2600	X-RAY DIFFRACTION	100
3.3077-3.4145	0.2536	105	0.2205	2629	X-RAY DIFFRACTION	100
3.4145-3.5365	0.2845	118	0.2145	2645	X-RAY DIFFRACTION	100
3.5365-3.678	0.239	136	0.2023	2605	X-RAY DIFFRACTION	100
3.678-3.8453	0.2312	139	0.2031	2617	X-RAY DIFFRACTION	100
3.8453-4.0479	0.2107	148	0.1776	2620	X-RAY DIFFRACTION	100
4.0479-4.3014	0.1603	168	0.1534	2592	X-RAY DIFFRACTION	100
4.3014-4.6332	0.18	139	0.1559	2639	X-RAY DIFFRACTION	100
4.6332-5.099	0.195	126	0.1663	2659	X-RAY DIFFRACTION	100
5.099-5.8356	0.2081	160	0.2122	2616	X-RAY DIFFRACTION	100
5.8356-7.3475	0.2259	146	0.2308	2683	X-RAY DIFFRACTION	100
7.3475-46.5163	0.1776	127	0.1881	2771	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	5.23	1.7812	2.0313	3.9789	0.4038	1.7741	-0.0914	1.1443	-0.1721	-0.5521	0.0568	0.1259	0.0663	0.5522	-0.1153	0.2679	0.0394	-0.012	1.1605	-0.0902	0.6011	-68.2343	-70.0337	-40.7168
2	1.8725	-0.3593	0.8939	0.1613	-0.1734	0.6809	-0.1336	0.3084	0.1442	-0.079	0.0216	-0.0336	-0.108	0.4269	0.0963	0.133	-0.1403	-0.0628	0.9767	-0.143	0.4811	-79.3904	-61.4754	-40.1137
3	6.0718	-0.9014	0.4751	5.5143	3.2489	2.8806	-0.4802	0.119	1.1571	-0.7129	0.2614	-0.1028	-1.3618	0.2481	0.0664	0.9065	-0.2954	-0.3415	0.6832	0.1143	1.0758	-92.8449	-35.5088	-46.7342
4	2.7617	-0.9778	1.7082	1.3108	-0.3157	1.3143	-0.2788	-0.014	0.2119	0.049	0.2046	-0.1884	-0.1951	0.1377	0.2281	-0.0022	-0.0824	-0.0893	0.9275	-0.1072	0.4477	-82.8046	-59.0228	-29.019
5	8.6075	1.0154	0.065	2.4035	-0.0485	2.6988	-0.079	-0.4665	-0.1087	0.2038	0.2432	-0.1689	0.1779	0.0674	-0.1649	0.1677	0.0842	-0.0626	0.8753	-0.0897	0.39	-65.7939	-69.3004	-17.9339
6	5.7923	0.9514	-0.9664	2.1188	1.6976	3.9045	-0.0607	-0.1616	0.5994	-0.1696	0.4947	0.0922	-0.2501	-0.23	-0.103	0.1871	0.0965	-0.0498	0.4553	-0.0019	0.3622	-35.7643	-60.5797	-3.2924
7	3.7586	-0.154	1.531	1.1681	-0.9501	2.8432	-0.0423	0.3495	0.0611	0.1133	0.3054	0.5075	0.1696	-0.2498	-0.1726	0.2098	0.0566	-0.0429	0.5903	-0.0484	0.49	-44.6778	-66.2621	-14.2523
8	2.901	0.1837	0.304	0.9796	0.342	1.517	-0.1612	0.5246	-0.0523	0.005	0.1319	-0.0076	-0.1525	-0.0307	0.0176	0.2236	0.1327	0.0064	0.611	-0.0162	0.487	-34.4576	-61.1605	-12.1779
9	1.5069	-0.0658	-0.4299	6.7482	0.3308	6.6392	0.3212	0.1641	0.5452	-0.0918	0.1953	-0.4823	-0.5903	0.2063	-0.4654	0.3048	0.1239	0.1465	0.5584	-0.0146	0.595	-18.3838	-43.4285	-14.278
10	4.024	0.3067	0.3611	8.6347	0.472	7.4827	0.0795	-0.1944	1.1975	-0.0578	0.7302	-0.3896	-1.8831	0.0404	-0.4466	0.7226	-0.0322	0.2445	0.6516	-0.0107	1.1179	-18.2845	-33.5972	-16.1802
11	3.1975	1.2057	-0.1971	1.9895	0.0811	1.0992	-0.0393	0.6223	0.2694	-0.2808	0.1104	0.0807	-0.0153	0.1659	-0.1076	0.152	0.031	-0.0022	0.7551	-0.0982	0.4095	-27.8941	-63.751	-24.9081
12	3.6155	0.9264	-0.8389	2.9446	-0.766	0.307	-0.1464	1.2558	-0.2238	-0.3308	0.3942	0.1371	0.1181	-0.1263	0.3538	0.2108	0.0011	0.0605	1.1584	-0.0867	0.3834	-31.0412	-67.672	-35.4226
13	7.3621	-1.4722	0.3036	3.5166	0.1901	1.978	-0.0105	0.5769	-0.3181	-0.2716	0.1921	-0.0583	0.0752	-0.2847	-0.1076	0.14	-0.0515	-0.0047	0.951	-0.1422	0.2939	-45.5901	-70.7168	-28.4877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 258:302)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 303:382)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 383:401)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 402:527)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 528:606)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 257:276)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 277:302)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 303:356)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 357:382)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 383:429)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 430:514)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 515:544)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 545:605)

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