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

ID or keywords:

Entry

Database: PDB / ID: 3ssm

Title

MycE Methyltransferase from the Mycinamycin Biosynthetic Pathway in Complex with Mg and SAH, Crystal form 1

Components

Methyltransferase

Keywords

TRANSFERASE / methyltransferase / macrolide / natural product / Rossmann Fold

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 /

SAD / Resolution: 2.247 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 12, 2014	Group: Structure summary
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.4	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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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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Download

PDBx/mmCIF format	3ssm.cif.gz	639.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ssm.ent.gz	532.3 KB	Display	PDB format
PDBx/mmJSON format	3ssm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ssm_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3ssm_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3ssm_validation.xml.gz	59.9 KB	Display
Data in CIF	3ssm_validation.cif.gz	86.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/3ssm ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3ssm	HTTPS FTP

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Related structure data

Related structure data	3ssnC 3ssoC C: citing same article (ref.)
Similar structure data	3sso-2 3ssn-d 1muk-d 1mwh-d 1n1h-d 2qhf-1 4red-1 2o12-2 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

189 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)	73.914, 143.407, 84.641
Angle α, β, γ (deg.)	90.000, 105.600, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#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
#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 845 / 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: 2.3 Å³/Da / Density % sol: 46.44 %
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: 0.97934 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2010

Radiation

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

Radiation wavelength

Wavelength: 0.97934 Å / Relative weight: 1

Reflection

Redundancy: 20.4 % / Av σ(I) over netI: 13.4 / Number: 1058098 / R_merge(I) obs: 0.182 / Χ²: 1.64 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 51769 / % possible obs: 100

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
5.6	50	100	1	0.079	1.794	21.2
4.45	5.6	100	1	0.106	2.052	21.4
3.88	4.45	100	1	0.125	2.053	21.3
3.53	3.88	100	1	0.162	1.928	21.4
3.28	3.53	100	1	0.228	1.762	21.4
3.08	3.28	100	1	0.319	1.514	21.4
2.93	3.08	100	1	0.426	1.395	21.4
2.8	2.93	100	1	0.595	1.296	21.4
2.69	2.8	100	1	0.787	1.234	20
2.6	2.69	100	1	0.998	1.184	13.5

Reflection

Resolution: 2.247→81.523 Å / Num. all: 80361 / Num. obs: 80345 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / B_iso Wilson estimate: 35.4 Å² / R_merge(I) obs: 0.087 / Χ²: 0.904 / Net I/σ(I): 7.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.247-2.33	3.9	0.614	8021	1.047	1	100
2.33-2.42	3.9	0.506	7984	1.018	1	100
2.42-2.53	3.9	0.398	8008	1.008	1	100
2.53-2.67	3.9	0.289	8027	1.001	1	100
2.67-2.83	3.9	0.215	8026	1.014	1	100
2.83-3.05	3.9	0.145	7982	1.023	1	100
3.05-3.36	3.9	0.095	8054	0.939	1	100
3.36-3.85	3.9	0.058	8048	0.776	1	100
3.85-4.85	3.9	0.045	8034	0.764	1	100
4.85-50	3.9	0.031	8161	0.46	1	99.9

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Phasing

Phasing

Method:

SAD

Phasing dm

FOM : 0.32 / FOM acentric: 0.32 / FOM centric: 0.33 / Reflection: 50213 / Reflection acentric: 48971 / Reflection centric: 1242

Phasing dm shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
7.4-50	0.77	0.78	0.66	2267	2103	164
4.6-7.4	0.61	0.61	0.47	6920	6658	262
3.7-4.6	0.53	0.54	0.41	8666	8433	233
3.2-3.7	0.32	0.32	0.28	8641	8455	186
2.8-3.2	0.14	0.14	0.1	15226	14959	267
2.6-2.8	0.07	0.07	0.05	8493	8363	130

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
SOLVE	2.13	phasing
RESOLVE	2.15	phasing
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
DENZO		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 2.247→81.52 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.942 / WR_factor R_free: 0.2135 / WR_factor R_work: 0.1659 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8753 / SU B: 11.974 / SU ML: 0.135 / SU R Cruickshank DPI: 0.2719 / SU R_free: 0.1973 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.197 / 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	0.2098	4019	5 %	RANDOM
R_work	0.1649	-	-	-
obs	0.1672	76211	99.47 %	-

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: 183.06 Å² / B_iso mean: 41.7704 Å² / B_iso min: 14.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	0.46 Å²
2-	-	-0.89 Å²	0 Å²
3-	-	-	1.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.247→81.52 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11915	0	81	845	12841

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.021	12315
X-RAY DIFFRACTION	r_angle_refined_deg	1.029	1.96	16707
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.201	5	1488
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.093	22.798	629
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.702	15	1947
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.497	15	123
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	1767
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	9666
X-RAY DIFFRACTION	r_mcbond_it	1.083	3.5	7437
X-RAY DIFFRACTION	r_mcangle_it	1.812	5	11976
X-RAY DIFFRACTION	r_scbond_it	1.261	3.5	4878
X-RAY DIFFRACTION	r_scangle_it	1.847	5	4731

LS refinement shell

Resolution: 2.247→2.306 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	264	-
R_work	0.223	5361	-
all	-	5625	-
obs	-	-	94.41 %

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	1.6459	0.2266	0.4603	0.8419	0.3327	2.0076	0.075	-0.2019	0.0612	0.2414	-0.094	0.2564	-0.0005	-0.0005	0.019	0.1201	-0.0221	0.0799	0.044	-0.0214	0.0988	-1.384	151.682	55.991
2	33.4991	-19.7468	17.1693	26.9216	-13.0972	9.4917	-1.5422	-1.7541	2.9274	2.1692	0.0489	-1.9198	-1.3176	0.4707	1.4933	0.6107	-0.6526	-0.2148	2.137	-0.1374	0.28	18.721	155.964	72.655
3	0.0737	0.2338	-0.0182	1.6186	0.5869	0.9044	-0.0031	-0.0599	-0.049	0.1375	0.0559	0.0045	-0.0039	0.1563	-0.0528	0.1222	0.0061	0.0249	0.1839	0.0064	0.1663	5.77	131.597	51.29
4	0.6276	0.1535	-0.4815	2.0391	0.0478	1.1402	0.0047	0.0374	-0.0876	0.0992	-0.0345	0.3278	0.0911	-0.1285	0.0298	0.0189	-0.0273	0.0072	0.0516	-0.015	0.2044	-12.006	122.475	42.245
5	0.9475	-0.3417	-0.1395	1.4342	0.3972	2.1376	0.0446	0.3305	-0.3494	-0.4955	-0.0001	0.333	-0.0143	-0.1162	-0.0444	0.2327	-0.0631	-0.0942	0.1972	-0.1505	0.2382	-4.634	118.07	16.153
6	1.7454	0.1208	-0.0139	4.2883	0.1589	2.206	-0.0718	0.2744	0.0572	-0.8072	0.186	0.6152	0.0856	-0.1045	-0.1142	0.1932	-0.0405	-0.1902	0.112	0.0168	0.2131	-12.703	142.324	17.458
7	3.7561	-1.2585	4.019	13.3998	7.4635	12.4527	0.0979	0.7401	-0.5169	-1.7468	-0.1781	0.0701	0.1805	0.306	0.0802	0.9133	-0.1901	0.1375	0.4967	-0.1357	0.4322	-5.166	131.347	2.898
8	7.3863	1.4079	2.774	0.8131	-0.0751	6.8074	-0.1599	0.7996	-0.556	-0.2837	0.4133	-0.5698	-0.3221	0.7903	-0.2535	0.4337	-0.0629	0.1432	0.4303	-0.3477	0.5466	6.625	149.56	17.598
9	2.123	0.0996	0.4775	2.3835	0.0284	1.3293	0.0207	0.1976	0.1929	-0.2641	0.0295	0.1387	-0.2242	0.0724	-0.0501	0.0947	0.0029	-0.0111	0.0419	0.0192	0.0895	3.349	164.03	27.799
10	2.2949	-0.0801	1.4347	1.2444	-0.1224	1.8123	0.0085	-0.2726	0.2227	0.2362	-0.0573	-0.0189	-0.1933	0.0096	0.0488	0.1279	-0.0811	0.0276	0.0941	-0.0444	0.0519	19.721	164.592	49.254
11	2.187	0.7425	-0.4719	1.9085	-0.3983	1.9096	0.12	-0.1418	-0.2561	0.294	-0.0742	-0.2809	0.0752	0.1849	-0.0458	0.0903	0.0428	-0.0634	0.0783	0.027	0.1618	24.244	119.586	48.17
12	11.3442	0.0971	-5.0909	12.0831	-0.3076	13.4292	0.3172	-1.4195	-1.0722	2.1963	0.0989	0.9292	0.6263	-0.8947	-0.4161	0.4946	-0.1494	0.0497	0.5279	0.1864	0.2982	7.489	111.419	64.233
13	0.201	-0.1188	-0.0037	3.9188	0.4245	0.0939	0.0373	-0.066	-0.0461	0.4444	-0.0693	0.0849	0.0632	0.0887	0.0319	0.1307	-0.0105	0.0189	0.1942	0.0406	0.1114	17.773	140.435	52.42
14	0.7172	0.4717	0.0173	2.5687	0.5105	0.6528	0.0774	-0.0275	-0.047	0.3003	0.0126	-0.3352	-0.0064	0.2274	-0.09	0.0499	-0.0433	-0.056	0.1741	-0.004	0.115	33.153	149.78	46.246
15	1.3702	-1.0831	0.6904	3.0454	3.1982	6.3426	0.1118	0.3095	0.1399	-0.6738	0.0189	-0.2212	-0.9974	0.6409	-0.1307	0.2473	-0.1435	0.0453	0.2214	0.0073	0.1224	27.855	157.462	29.577
16	0.6369	-0.1661	-0.2348	2.43	-0.918	2.048	-0.0669	0.2022	-0.0654	-0.31	0.0371	-0.1882	0.0465	0.0035	0.0299	0.0627	-0.0496	0.0519	0.2063	-0.0274	0.0584	29.569	140.505	14.026
17	2.5877	-0.9713	0.4357	9.2403	-5.3601	7.6458	0.1448	0.275	0.3875	0.0073	0.0087	0.4354	-1.0686	-0.7871	-0.1534	0.3142	0.1448	0.0089	0.2697	0.0123	0.0992	21.717	155.697	6.391
18	10.2037	2.8298	-2.6131	3.3063	-0.9342	1.3905	-0.1823	1.1091	0.2515	-1.0136	-0.1002	0.088	-0.0259	-0.3012	0.2825	0.5004	0.0652	-0.0391	0.2892	0.0316	0.287	4.32	129.926	14.381
19	2.0723	1.0401	-0.1249	2.6071	0.3809	1.1181	-0.1863	0.3896	-0.2006	-0.5065	0.1893	0.052	0.1447	0.1238	-0.003	0.1597	-0.0181	0.0017	0.1156	-0.0739	0.0755	12.295	115.956	16.902
20	1.6272	0.0564	-1.2988	1.1694	0.0751	2.8055	-0.1289	-0.0834	-0.3789	0.0193	-0.0195	0.0522	0.4223	0.179	0.1484	0.1059	0.0104	-0.0004	0.0173	0.0046	0.2126	1.335	108.602	39.874

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 128
2	X-RAY DIFFRACTION	2	A	129 - 142
3	X-RAY DIFFRACTION	3	A	143 - 190
4	X-RAY DIFFRACTION	4	A	191 - 363
5	X-RAY DIFFRACTION	5	A	364 - 395
6	X-RAY DIFFRACTION	6	B	6 - 132
7	X-RAY DIFFRACTION	7	B	133 - 156
8	X-RAY DIFFRACTION	8	B	157 - 182
9	X-RAY DIFFRACTION	9	B	183 - 326
10	X-RAY DIFFRACTION	10	B	327 - 397
11	X-RAY DIFFRACTION	11	C	6 - 127
12	X-RAY DIFFRACTION	12	C	128 - 147
13	X-RAY DIFFRACTION	13	C	148 - 187
14	X-RAY DIFFRACTION	14	C	188 - 337
15	X-RAY DIFFRACTION	15	C	338 - 382
16	X-RAY DIFFRACTION	16	D	5 - 127
17	X-RAY DIFFRACTION	17	D	128 - 160
18	X-RAY DIFFRACTION	18	D	161 - 185
19	X-RAY DIFFRACTION	19	D	186 - 320
20	X-RAY DIFFRACTION	20	D	321 - 397

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+About Yorodumi

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-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

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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

-
Phasing

-
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

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Yorodumi