PDB-3ssn: MycE Methyltransferase from the Mycinamycin Biosynthetic Pathway ...

ID or keywords:

Entry

Database: PDB / ID: 3ssn

Title

MycE Methyltransferase from the Mycinamycin Biosynthetic Pathway in Complex with Mg, SAH, and Mycinamycin VI

Components

Methyltransferase

Keywords

TRANSFERASE/ANTIBIOTIC / methyltransferase / macrolide / natural product / Rossmann Fold / TRANSFERASE-ANTIBIOTIC complex

Function / homology

Function and homology information

mycinamicin VI 2''-O-methyltransferase / mycinamicin VI 2''-O-methyltransferase activity / O-methyltransferase activity / antibiotic biosynthetic process / methylation / protein homotetramerization / magnesium ion binding
Similarity search - Function

Biological species

Micromonospora griseorubida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.392 Å

Authors

Akey, D.L. / Smith, J.L.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: A new structural form in the SAM/metal-dependent o‑methyltransferase family: MycE from the mycinamicin biosynthetic pathway.
Authors: Akey, D.L. / Li, S. / Konwerski, J.R. / Confer, L.A. / Bernard, S.M. / Anzai, Y. / Kato, F. / Sherman, D.H. / Smith, J.L.

History

Deposition	Jul 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 24, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 28, 2011	Group: Database references
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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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Validation report

Summary document	3ssn_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	3ssn_full_validation.pdf.gz	1.6 MB	Display
Data in XML	3ssn_validation.xml.gz	58.3 KB	Display
Data in CIF	3ssn_validation.cif.gz	81.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/3ssn ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3ssn	HTTPS FTP

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Related structure data

Related structure data	3ssmC 3ssoC C: citing same article (ref.)
Similar structure data	3ssm-d 3m0v-d 3itx-d 3iui-d 3sso-2 2hcv-d 3m0m-d 3m0l-d 3m0y-d 4red-1 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: Methyltransferase

B: Methyltransferase

C: Methyltransferase

D: Methyltransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	73.113, 142.111, 83.857
Angle α, β, γ (deg.)	90.000, 105.610, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Methyltransferase Mass: 47035.613 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycE / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q83WF2, Transferases; Transferring one-carbon groups; Methyltransferases

#1: Protein

Methyltransferase

Mass: 47035.613 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Micromonospora griseorubida (bacteria) / Gene: mycE / Plasmid: pET28b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q83WF2, Transferases; Transferring one-carbon groups; Methyltransferases

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Non-polymers , 6 types, 534 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Chemical	ChemComp-MVI / Mycinamicin VI / [(2R,3R,4E,6E,9R,11S,12S,13S,14E)-2-ethyl-9,11,13-trimethyl-8,16-dioxo-12-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}oxacyclohexadeca-4,6,14-trien-3-yl]methyl 6-deoxy-beta-D-allopyranoside Mass: 667.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₅H₅₇NO₁₁
#5: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.23 Å³/Da / Density % sol: 44.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 20%-25% PEG 3350, 0.15 M NaCl, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 1.0331 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 19, 2010

Radiation

Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.0331 Å / Relative weight: 1

Reflection

Resolution: 2.392→50 Å / Num. all: 64796 / Num. obs: 64220 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / R_merge(I) obs: 0.077 / Χ²: 0.997 / Net I/σ(I): 8.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.392-2.49	3.3	0.688	6396	1.217	1	99.3
2.49-2.59	3.3	0.521	6449	1.21	1	99.4
2.59-2.7	3.4	0.398	6404	1.258	1	99.3
2.7-2.85	3.4	0.294	6416	1.175	1	99.6
2.85-3.02	3.4	0.198	6432	1.137	1	99.6
3.02-3.26	3.4	0.131	6423	1.034	1	99.6
3.26-3.58	3.4	0.082	6433	0.94	1	99.4
3.58-4.1	3.4	0.06	6460	0.987	1	99.1
4.1-5.17	3.4	0.037	6395	0.605	1	98.7
5.17-50	3.4	0.028	6412	0.423	1	97.4

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
DENZO		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.392→46.7 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.941 / WR_factor R_free: 0.2228 / WR_factor R_work: 0.1684 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8516 / SU B: 17.094 / SU ML: 0.181 / SU R Cruickshank DPI: 0.4453 / SU R_free: 0.2427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2181	3260	5.1 %	RANDOM
R_work	0.1654	-	-	-
obs	0.1681	64131	98.66 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso max: 186.76 Å² / B_iso mean: 50.8588 Å² / B_iso min: 17.69 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.58 Å²	0 Å²	1.24 Å²
2-	-	-0.73 Å²	0 Å²
3-	-	-	0.81 Å²

Refinement step

Cycle: LAST / Resolution: 2.392→46.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11901	0	193	522	12616

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	12400
X-RAY DIFFRACTION	r_angle_refined_deg	1.133	1.973	16824
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.474	5	1485
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.778	22.866	628
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.493	15	1944
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.442	15	121
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1801
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	9669
X-RAY DIFFRACTION	r_mcbond_it	1.272	3.5	7425
X-RAY DIFFRACTION	r_mcangle_it	2.115	5	11959
X-RAY DIFFRACTION	r_scbond_it	1.45	3.5	4975
X-RAY DIFFRACTION	r_scangle_it	2.166	5	4865

LS refinement shell

Resolution: 2.392→2.454 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	235	-
R_work	0.238	4258	-
all	-	4493	-
obs	-	-	93.92 %

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	11.617	4.4271	-0.9517	13.5773	-1.3634	6.7393	0.1732	-0.4365	0.2419	0.4107	0.064	1.3345	0.0988	-0.9709	-0.2372	0.0842	0.027	0.0997	0.2452	-0.0207	0.4142	-14.266	145.422	49.414
2	2.5217	0.0454	0.7061	1.1528	0.0106	2.4124	0.0532	-0.2952	0.0707	0.32	-0.0967	0.1923	-0.2199	0.0988	0.0435	0.1495	-0.049	0.0956	0.0847	-0.0137	0.0894	3.51	151.193	58.007
3	1.5925	-0.6063	0.1453	3.7331	0.4658	3.8397	-0.1116	-0.1904	-0.143	0.2972	-0.0696	0.0405	0.2666	0.1231	0.1813	0.0535	-0.0049	0.0559	0.1334	0.0208	0.1774	4.048	125.165	48.354
4	0.9346	0.563	-0.2927	2.8544	-0.4098	1.8852	0.0458	-0.0705	-0.0701	0.2828	-0.1112	0.3404	0.1608	-0.2321	0.0654	0.0592	-0.0419	0.0889	0.1005	-0.0335	0.2945	-12.081	124.749	46.915
5	1.1098	0.1714	-0.2194	2.6073	-0.3377	2.7103	-0.1434	0.2329	-0.2536	-0.366	0.0126	0.4683	0.4427	-0.3944	0.1307	0.1292	-0.0882	0.0213	0.1359	-0.0749	0.3629	-9.83	115.095	29.494
6	6.5478	-1.0274	-6.7529	3.3971	7.6939	20.9638	-0.5112	0.989	-0.5543	0.2014	0.0137	0.1434	1.2233	-0.9633	0.4975	0.8809	-0.1199	-0.1787	0.5873	-0.1908	0.7067	-4.363	113.978	5.472
7	2.4039	0.6415	0.2005	3.5181	0.5752	3.3287	-0.1148	0.554	0.0879	-0.6775	0.1535	0.5299	-0.0308	-0.1257	-0.0387	0.1472	-0.0033	-0.1477	0.2433	0.0297	0.3465	-12.191	142.113	17.546
8	7.2484	1.922	2.7639	4.755	-1.4175	3.058	0.0383	1.8449	-1.2393	-1.7185	0.5241	-0.2925	0.7282	0.8517	-0.5625	1.0668	-0.0085	-0.1253	0.978	-0.2979	0.691	-7.611	128.908	1.986
9	3.8491	6.9449	0.6571	13.3199	0.5852	0.8099	-0.7577	0.7053	-0.8184	-1.5889	0.759	-1.3236	-0.0526	0.3567	-0.0013	0.5171	-0.0528	0.0793	0.7831	-0.2407	0.6744	5.883	146.603	17.691
10	3.9487	0.3241	0.3741	3.0863	0.0357	1.7677	0.1693	0.3701	0.0498	-0.4509	-0.0834	0.1899	-0.2857	0.1736	-0.086	0.1466	0.0196	0.0059	0.0877	-0.0088	0.1147	3.838	156.552	24.616
11	3.7625	0.8868	1.0051	2.7406	-0.0755	1.9462	0.1056	0.2453	0.3856	-0.2514	-0.0026	0.1524	-0.415	0.1171	-0.103	0.2251	0.0383	0.0429	0.0474	0.0206	0.2022	3.698	167.392	28.86
12	2.3797	-0.5157	1.6881	2.0767	-0.6403	3.1622	-0.0446	-0.338	0.212	0.4009	-0.0482	-0.0917	-0.61	0.2222	0.0928	0.2711	-0.1392	0.045	0.1618	-0.023	0.1634	19.91	163.143	48.638
13	2.9314	0.4418	-1.7094	2.3732	-0.4557	3.0773	0.0422	-0.3561	-0.2868	0.3703	-0.1037	-0.274	0.3222	0.4864	0.0615	0.1642	0.1106	-0.0454	0.2273	0.0695	0.2366	25.68	118.254	49.256
14	2.317	0.06	-0.5207	0.779	0.4194	2.6417	0.0302	-0.3749	-0.2444	0.3422	-0.1056	0.0826	0.4387	0.0892	0.0754	0.2479	0.0373	0.065	0.1614	0.0689	0.2408	12.592	117.002	50.814
15	1.3856	0.324	-0.0447	2.7937	0.1076	2.0084	0.039	-0.1369	-0.0887	0.5756	-0.0517	-0.3691	-0.0807	0.418	0.0127	0.1263	-0.0303	-0.0631	0.2262	0.0582	0.1693	30.095	141.956	49.132
16	0.9201	1.3103	1.0801	2.778	0.7704	2.0307	0.0342	0.0918	-0.0368	0.2837	-0.0697	-0.2618	-0.2764	0.4049	0.0355	0.1791	-0.1628	0.0086	0.3238	0.0349	0.2677	32.751	156.833	44.727
17	3.1777	-0.6838	1.7802	3.7382	0.7803	1.3991	-0.1027	0.2759	0.1948	-0.496	0.0703	-0.3226	-0.2646	0.2881	0.0324	0.2514	-0.179	0.0455	0.3613	0.0455	0.2287	28.188	158.586	35.279
18	1.0338	0.5277	3.1396	0.3077	1.7477	21.4607	-0.2671	0.3918	0.255	-0.2325	0.1041	0.1934	-2.7054	0.4671	0.163	0.7956	-0.0285	-0.0324	0.6706	0.0679	0.4624	28.748	156.412	20.437
19	1.204	-0.3863	0.0058	3.1817	-2.1556	3.8129	0.0052	0.2019	-0.1049	-0.4126	0.002	-0.2397	-0.027	0.1682	-0.0071	0.1365	-0.0086	0.1094	0.2977	-0.0132	0.1063	30.205	138.179	12.232
20	1.5521	-0.4399	0.0051	0.3912	0.4098	2.9853	0.0676	0.2614	0.2401	-0.2115	0.0204	0.0173	-0.6749	-0.1503	-0.088	0.3318	0.029	0.0871	0.328	0.0651	0.2118	21.921	149.252	12.512
21	12.1514	2.263	-3.5755	3.5802	-3.3625	3.3703	-0.4514	1.6765	-0.0623	-0.7766	0.4003	0.0316	0.6712	-0.6049	0.0511	0.6732	-0.0016	-0.0438	0.5595	-0.0089	0.5329	3.126	127.8	12.555
22	2.4776	0.9325	-0.2	3.3462	0.2237	2.2499	-0.1427	0.4149	-0.2653	-0.6364	0.0832	0.0919	0.3806	0.1522	0.0595	0.2419	0.0545	0.0379	0.1521	-0.0472	0.1612	14.262	115.989	16.555
23	2.7965	2.2575	-2.6259	2.8116	1.1542	15.4446	-0.4375	0.1036	0.0044	-0.1837	-0.3216	0.6999	1.6495	-0.9851	0.7592	0.6889	-0.0757	-0.1604	0.6787	-0.5396	1.7704	-7.215	105.878	17.018
24	0.9191	0.1702	-0.8752	1.5982	0.5161	2.6538	-0.1306	-0.1624	-0.2949	0.1731	-0.0298	0.0626	0.7563	0.0685	0.1604	0.259	-0.0151	0.052	0.0658	0.0286	0.2879	1.444	108.025	40.702

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 19
2	X-RAY DIFFRACTION	2	A	20 - 159
3	X-RAY DIFFRACTION	3	A	160 - 189
4	X-RAY DIFFRACTION	4	A	190 - 315
5	X-RAY DIFFRACTION	5	A	316 - 375
6	X-RAY DIFFRACTION	6	A	376 - 395
7	X-RAY DIFFRACTION	7	B	6 - 126
8	X-RAY DIFFRACTION	8	B	127 - 156
9	X-RAY DIFFRACTION	9	B	157 - 171
10	X-RAY DIFFRACTION	10	B	182 - 239
11	X-RAY DIFFRACTION	11	B	240 - 327
12	X-RAY DIFFRACTION	12	B	328 - 396
13	X-RAY DIFFRACTION	13	C	6 - 104
14	X-RAY DIFFRACTION	14	C	105 - 161
15	X-RAY DIFFRACTION	15	C	162 - 266
16	X-RAY DIFFRACTION	16	C	267 - 326
17	X-RAY DIFFRACTION	17	C	327 - 368
18	X-RAY DIFFRACTION	18	C	369 - 382
19	X-RAY DIFFRACTION	19	D	5 - 107
20	X-RAY DIFFRACTION	20	D	108 - 165
21	X-RAY DIFFRACTION	21	D	166 - 185
22	X-RAY DIFFRACTION	22	D	186 - 305
23	X-RAY DIFFRACTION	23	D	306 - 327
24	X-RAY DIFFRACTION	24	D	328 - 397

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Components

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 6 types, 534 molecules

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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