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

ID or keywords:

Entry

Database: PDB / ID: 3sso

Title

MycE Methyltransferase from the Mycinamycin Biosynthetic Pathway in Complex with Mg and SAH, Crystal form 2

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 /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.895 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	3sso.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb3sso.ent.gz	900.3 KB	Display	PDB format
PDBx/mmJSON format	3sso.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3sso_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	3sso_full_validation.pdf.gz	1.8 MB	Display
Data in XML	3sso_validation.xml.gz	108.9 KB	Display
Data in CIF	3sso_validation.cif.gz	164.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/3sso ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3sso	HTTPS FTP

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Related structure data

Related structure data	3ssmC 3ssnC C: citing same article (ref.)
Similar structure data	3ssn-d 1lm1-d 3ahh-1 3f5m-d 1ofe-1 1ofe-2 1wql-1 1llz-d 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

Deposited unit

A: Methyltransferase

B: Methyltransferase

C: Methyltransferase

D: Methyltransferase

E: Methyltransferase

F: Methyltransferase

hetero molecules

285 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyltransferase

B: Methyltransferase

C: Methyltransferase

D: Methyltransferase

hetero molecules

defined by author&software
190 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Methyltransferase

F: Methyltransferase

hetero molecules

E: Methyltransferase

F: Methyltransferase

hetero molecules

defined by author&software
190 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	144.220, 250.846, 158.315
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	E-1495- HOH

#1: Protein	Methyltransferase Mass: 47035.613 Da / Num. of mol.: 6 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.: 6 / 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.: 6 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2780 / 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: 2.54 Å³/Da / Density % sol: 51.51 %
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: 1.0332 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 11, 2009

Radiation

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

Radiation wavelength

Wavelength: 1.0332 Å / Relative weight: 1

Reflection

Resolution: 1.895→50 Å / Num. all: 225078 / Num. obs: 216642 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / B_iso Wilson estimate: 22.8 Å² / R_merge(I) obs: 0.121 / Χ²: 1.782 / Net I/σ(I): 9.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.895-1.97	3.8	0.511	17039	1.275	1	76.3
1.97-2.05	4.8	0.398	19748	1.445	1	88.4
2.05-2.14	6.2	0.309	21861	1.578	1	97.7
2.14-2.25	7.3	0.252	22333	1.725	1	100
2.25-2.39	7.4	0.205	22404	1.824	1	100
2.39-2.58	7.5	0.173	22477	1.829	1	100
2.58-2.84	7.5	0.15	22471	1.986	1	100
2.84-3.25	7.5	0.125	22547	2.088	1	100
3.25-4.09	7.5	0.106	22622	2.053	1	100
4.09-50	7.4	0.084	23140	1.471	1	99.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER		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:

MOLECULAR REPLACEMENT / Resolution: 1.895→49.16 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / WR_factor R_free: 0.1872 / WR_factor R_work: 0.1528 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9005 / SU B: 5.314 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1217 / SU R_free: 0.1123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.112 / 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	0.1765	10937	5 %	RANDOM
R_work	0.1436	-	-	-
obs	0.1453	216609	100 %	-

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: 102.85 Å² / B_iso mean: 28.8522 Å² / B_iso min: 10.37 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0 Å²	0 Å²	0 Å²
2-	-	-0.09 Å²	0 Å²
3-	-	-	0.09 Å²

Refinement step

Cycle: LAST / Resolution: 1.895→49.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18768	0	162	2780	21710

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.021	20217
X-RAY DIFFRACTION	r_angle_refined_deg	1.061	1.959	27561
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.33	5	2511
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.785	22.779	1047
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.068	15	3192
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.749	15	213
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	2859
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.021	16215
X-RAY DIFFRACTION	r_mcbond_it	1.501	5	12210
X-RAY DIFFRACTION	r_mcangle_it	2.273	8	19773
X-RAY DIFFRACTION	r_scbond_it	1.95	5	8007
X-RAY DIFFRACTION	r_scangle_it	2.898	8	7788

LS refinement shell

Resolution: 1.895→1.944 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.288	487	-
R_work	0.224	11331	-
all	-	11818	-
obs	-	-	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	0.922	-0.5194	0.1339	1.4804	-0.6125	1.6977	-0.16	-0.1924	0.1122	0.279	0.1213	-0.0236	-0.1322	-0.1266	0.0387	0.079	0.0378	-0.0375	0.0818	-0.0241	0.048	-40.276	-66.938	19.774
2	1.6903	-0.8084	0.5572	1.0303	0.266	0.6754	-0.1585	-0.61	-0.2569	0.1367	0.2191	0.1744	0.1006	-0.2785	-0.0607	0.237	0.0469	0.0139	0.3237	0.1007	0.1137	-51.466	-76.376	25.263
3	0.729	-0.0708	0.0445	0.445	0.1236	0.1719	-0.0125	-0.0252	0.0425	0.029	0.0167	0.0167	0.0033	-0.0334	-0.0042	0.0303	0.0141	-0.0161	0.0356	0.0135	0.0437	-63.137	-60.707	0.745
4	0.5024	-0.0944	0.1351	0.4998	0.2488	0.8649	-0.0043	0.2156	0.021	-0.1262	-0.0031	0.0712	-0.0877	-0.0075	0.0075	0.0594	-0.0011	-0.0356	0.1346	0.0205	0.0312	-63.255	-70.135	-24.202
5	1.7456	-1.2022	0.1188	1.9215	-0.0755	0.4677	-0.1544	-0.4192	-0.2471	0.1917	0.2709	0.2532	-0.0411	-0.1647	-0.1164	0.0359	0.0273	0.0205	0.1699	0.0968	0.0969	-74.259	-90.664	11.607
6	1.6916	0.2338	1.2286	0.0528	0.2634	1.3714	-0.1159	-0.3206	0.1425	-0.0213	-0.0255	0.032	-0.1797	-0.2276	0.1414	0.1765	0.0687	0.0033	0.1899	0.0523	0.1799	-55.169	-84.504	19.54
7	0.8888	-0.0271	0.4324	0.4649	-0.1458	1.0471	-0.0436	-0.1568	-0.1449	0.105	0.088	0.0832	0.0741	-0.1106	-0.0444	0.1052	0.0299	0.0097	0.088	0.0751	0.0852	-45.19	-102.8809	21.9696
8	1.0032	-0.069	-0.3328	0.27	-0.1489	0.3448	-0.033	0.0276	-0.1941	-0.0012	0.0175	-0.0478	0.0619	-0.0071	0.0155	0.0839	0.0237	-0.0197	0.0458	-0.0106	0.1174	-23.2643	-104.0301	3.8651
9	1.8176	0.0925	0.6299	0.6258	0.1918	1.8025	0.0272	0.3799	0.059	-0.0895	-0.053	-0.1025	0.0761	0.1749	0.0258	0.0571	0.0222	0.0003	0.1165	0.0472	0.0493	-36.878	-68.867	-20.29
10	1.7539	-0.5157	0.0535	0.7909	-0.4017	0.305	0.2459	0.3694	-0.2317	-0.2237	-0.2238	0.1322	0.1844	0.0266	-0.0221	0.2331	0.0529	-0.0627	0.2653	-0.0583	0.1007	-40.051	-83.085	-25.317
11	0.5616	-0.1228	-0.0632	0.653	-0.1118	0.1676	-0.004	0.0318	-0.0153	-0.0159	0.0042	-0.0581	0.0219	0.0277	-0.0002	0.0189	0.0132	-0.0129	0.0439	0.0048	0.044	-20.11	-85.689	-0.428
12	0.5618	0.0846	-0.2118	0.4788	-0.4073	1.0731	-0.0079	-0.1265	-0.0678	0.1922	0.0176	-0.0564	-0.045	0.0709	-0.0097	0.1183	0.0375	-0.0292	0.0774	0.026	0.0387	-29.462	-89.696	24.923
13	3.2069	-0.452	0.1851	0.7956	-0.1219	0.4764	0.2288	0.4884	-0.3466	-0.201	-0.1315	0.071	0.135	0.1282	-0.0973	0.1226	0.0693	-0.057	0.0991	-0.0637	0.0984	-41.0082	-110.1554	-12.1583
14	0.6727	-1.186	0.663	2.1659	-1.3859	1.3105	0.1006	0.1328	0.0611	-0.17	-0.256	-0.1394	0.1035	0.26	0.1554	0.098	0.0349	-0.0354	0.1967	-0.0201	0.1367	-45.713	-90.172	-19.326
15	0.711	-0.2694	0.3275	0.9139	-0.3578	0.9251	0.0804	0.1825	-0.1464	-0.1106	-0.038	0.1042	0.1276	0.0072	-0.0424	0.0756	0.0067	-0.0592	0.1208	-0.0433	0.0738	-66.455	-90.706	-22.268
16	0.8466	-0.3315	-0.0718	1.013	0.5807	0.4922	-0.0081	0.0151	-0.0772	0.0341	-0.0424	0.2467	0.0335	-0.0898	0.0506	0.0607	-0.0021	-0.0084	0.1082	0.0353	0.1204	-78.069	-72.64	-3.929
17	0.8296	-0.741	-0.0254	2.9473	0.2429	0.6033	0.0841	0.0939	0.0984	-0.5556	0.0151	-0.3901	-0.1547	0.0439	-0.0992	0.1377	-0.036	0.0956	0.0543	-0.0237	0.1228	44.6099	-108.5105	-11.1348
18	1.2909	0.3858	-0.2403	2.4033	1.3894	0.9834	-0.2083	0.0401	0.0536	-1.0408	0.0615	0.2751	-0.5686	-0.003	0.1468	0.6511	0.01	-0.0772	0.2589	0.0093	0.2864	31.0447	-102.3944	-16.306
19	0.6256	0.1911	-0.0504	0.8447	0.2727	0.7444	0.0483	0.0915	0.0093	-0.2215	0.0011	-0.1544	-0.0651	0.0638	-0.0494	0.1261	0.0266	0.0625	0.0748	-0.0287	0.0707	37.8949	-136.4461	-22.2109
20	0.4121	0.1976	-0.3105	0.937	-0.2533	0.391	0.0161	-0.0162	-0.1371	-0.0177	-0.0229	-0.1488	0.0418	0.0394	0.0068	0.0887	0.0192	-0.0287	0.0722	-0.0191	0.1357	30.0907	-156.7472	-4.5251
21	0.9826	-0.4839	-0.4501	1.4715	0.4635	1.8503	0.0925	0.1438	0.0402	-0.3518	-0.1217	0.0943	-0.1776	-0.03	0.0292	0.1227	0.0185	-0.0427	0.0538	-0.0208	0.0465	5.9666	-123.4281	-20.1848
22	0.3421	-0.1721	0.2429	2.2466	0.175	0.2943	-0.0708	0.0518	0.0094	-0.606	0.0985	-0.289	-0.1023	0.1867	-0.0277	0.3358	-0.0072	0.0806	0.242	-0.0267	0.1109	19.5652	-118.7691	-25.5932
23	0.5117	0.1127	0.1356	0.6719	-0.0227	0.0895	0.0143	0.0204	0.0544	-0.0397	-0.0102	0.0286	-0.0356	0.0053	-0.0041	0.0484	0.0029	0.0094	0.0179	-0.0196	0.0495	12.1374	-100.4355	-0.3365
24	0.6559	-0.0962	0.4508	0.6438	0.0273	0.7996	0.0389	-0.2043	0.0823	0.2366	-0.0457	-0.0094	-0.0502	-0.0885	0.0067	0.1466	-0.0465	0.0049	0.0958	-0.0417	0.0422	20.1448	-106.5764	25.1275

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 - 175
3	X-RAY DIFFRACTION	3	A	176 - 320
4	X-RAY DIFFRACTION	4	A	321 - 398
5	X-RAY DIFFRACTION	5	B	6 - 142
6	X-RAY DIFFRACTION	6	B	143 - 185
7	X-RAY DIFFRACTION	7	B	186 - 326
8	X-RAY DIFFRACTION	8	B	327 - 399
9	X-RAY DIFFRACTION	9	C	6 - 128
10	X-RAY DIFFRACTION	10	C	129 - 175
11	X-RAY DIFFRACTION	11	C	176 - 326
12	X-RAY DIFFRACTION	12	C	327 - 398
13	X-RAY DIFFRACTION	13	D	6 - 142
14	X-RAY DIFFRACTION	14	D	143 - 187
15	X-RAY DIFFRACTION	15	D	188 - 329
16	X-RAY DIFFRACTION	16	D	330 - 399
17	X-RAY DIFFRACTION	17	E	6 - 128
18	X-RAY DIFFRACTION	18	E	129 - 169
19	X-RAY DIFFRACTION	19	E	170 - 326
20	X-RAY DIFFRACTION	20	E	327 - 399
21	X-RAY DIFFRACTION	21	F	6 - 128
22	X-RAY DIFFRACTION	22	F	129 - 175
23	X-RAY DIFFRACTION	23	F	176 - 326
24	X-RAY DIFFRACTION	24	F	327 - 398

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