PDB-4x81: MycF mycinamicin III 3'-O-methyltransferase (E35Q, M56A, E139A va...

ID or keywords:

Entry

Database: PDB / ID: 4x81

Title

MycF mycinamicin III 3'-O-methyltransferase (E35Q, M56A, E139A variant) in complex with Mg, SAH and mycinamicin VI (MycE substrate)

Components

Mycinamicin III 3''-O-methyltransferase

Keywords

Transferase/Antibiotic / macrolide / methyltransferase / antibiotic / natural product / Transferase-Antibiotic complex

Function / homology

Function and homology information

mycinamicin III 3''-O-methyltransferase / O-methyltransferase activity / small molecule binding / antibiotic biosynthetic process / methylation / magnesium ion binding
Similarity search - Function

Biological species

Micromonospora griseorubida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.59 Å

Authors

Bernard, S.M. / Smith, J.L.

Citation

Journal: Acs Chem.Biol. / Year: 2015
Title: Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O-Methyltransferases.
Authors: Bernard, S.M. / Akey, D.L. / Tripathi, A. / Park, S.R. / Konwerski, J.R. / Anzai, Y. / Li, S. / Kato, F. / Sherman, D.H. / Smith, J.L.

History

Deposition	Dec 9, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2015	Provider: repository / Type: Initial release
Revision 1.1	May 27, 2015	Group: Database references
Revision 1.2	Jul 20, 2016	Group: Data collection
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 / pdbx_struct_oper_list / struct_conn 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.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.value / _pdbx_struct_oper_list.symmetry_operation / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x81.cif.gz	223.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4x81.ent.gz	178.7 KB	Display	PDB format
PDBx/mmJSON format	4x81.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4x81_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4x81_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4x81_validation.xml.gz	25.5 KB	Display
Data in CIF	4x81_validation.cif.gz	37.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/4x81 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x81	HTTPS FTP

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Related structure data

Related structure data	4x7uC 4x7vC 4x7wC 4x7xC 4x7yC 4x7zC 4xvyC 4xvzC C: citing same article (ref.)
Similar structure data	4x7z-d 4x7u-d 2arx-d 4qbh-d 4x7v-d 2phw-d 3v48-d 4x7w-d 2arb-d 2zi5-1 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: Mycinamicin III 3''-O-methyltransferase

B: Mycinamicin III 3''-O-methyltransferase

hetero molecules

63.9 kDa, 2 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)	50.269, 91.747, 127.774
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Mycinamicin III 3''-O-methyltransferase / Mycinamicin biosynthesis protein F Mass: 30697.424 Da / Num. of mol.: 2 / Mutation: E35Q, M56A, E139A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycF / Plasmid: pET28b-mycF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase

#1: Protein

Mycinamicin III 3''-O-methyltransferase / Mycinamicin biosynthesis protein F

Mass: 30697.424 Da / Num. of mol.: 2 / Mutation: E35Q, M56A, E139A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

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

Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase

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Non-polymers , 5 types, 497 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: 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
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.74 %
Crystal grow	Temperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20-30% PEG 5000 MME, 100 mM ammonium acetate, and 100 mM BisTrisPropane pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2014
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.59→50 Å / Num. obs: 79006 / % possible obs: 98.5 % / Redundancy: 6.6 % / Net I/σ(I): 12.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Resolution: 1.59→50 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.966 / SU B: 3.093 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18833	3860	4.9 %	RANDOM
R_work	0.16826	-	-	-
obs	0.16925	75134	98.52 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.192 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.02 Å²	-0 Å²	0 Å²
2-	-	1.25 Å²	-0 Å²
3-	-	-	-0.23 Å²

Refinement step

Cycle: LAST / Resolution: 1.59→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3958	0	164	487	4609

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	4261
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3930
X-RAY DIFFRACTION	r_angle_refined_deg	1.31	1.96	5803
X-RAY DIFFRACTION	r_angle_other_deg	0.799	3	9009
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.634	5	508
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.115	23.048	210
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.525	15	643
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.59	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	645
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	4848
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1020
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.709	1.306	2029
X-RAY DIFFRACTION	r_mcbond_other	0.709	1.305	2028
X-RAY DIFFRACTION	r_mcangle_it	1.155	1.953	2538
X-RAY DIFFRACTION	r_mcangle_other	1.155	1.953	2539
X-RAY DIFFRACTION	r_scbond_it	1.38	1.618	2232
X-RAY DIFFRACTION	r_scbond_other	1.38	1.62	2233
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.193	2.36	3266
X-RAY DIFFRACTION	r_long_range_B_refined	5.489	12.649	5279
X-RAY DIFFRACTION	r_long_range_B_other	5.49	12.657	5280
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.59→1.632 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.351	266	-
R_work	0.342	5313	-
obs	-	-	95.42 %

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	0.0932	0.0808	0.1895	1.8419	-0.6924	0.8022	-0.0014	-0.0609	0.0217	0.1187	-0.0309	0.0351	-0.0513	-0.1438	0.0323	0.0633	-0.0075	-0.0169	0.0804	-0.0076	0.0114	22.3084	-4.7479	127.525
2	0.3528	0.3528	0.3499	1.3893	0.2881	0.4268	-0.0316	-0.0101	0.0547	-0.0099	0.0073	0.09	0.0245	-0.038	0.0243	0.0452	-0.0078	-0.0208	0.0808	-0.0044	0.0215	23.6509	-3.7806	133.774
3	0.338	-0.1122	0.3728	0.887	0.0675	0.4641	-0.0564	0.0725	0.0289	-0.0654	0.0157	0.0312	-0.0596	0.1008	0.0408	0.058	-0.0145	-0.005	0.0771	0.0068	0.0151	36.2965	5.4838	132.1341
4	0.4466	0.0011	0.9005	0.9266	-0.8147	3.7628	0.0353	0.0299	-0.0493	-0.0018	-0.0164	-0.0388	0.123	-0.0023	-0.0189	0.0467	0.0159	-0.0046	0.0219	-0.0012	0.0318	38.1482	-17.5937	144.0776
5	0.3495	-0.182	0.2128	0.6805	0.3338	1.2287	0.004	0.0968	0.0013	-0.0835	0.0302	-0.0655	0.0002	0.2418	-0.0342	0.0187	-0.0123	0.0102	0.1074	-0.0063	0.0075	43.4065	-1.4109	131.6157
6	0.5809	0.4287	0.0769	0.6402	-0.2796	0.3766	0.0137	-0.0346	0.0168	0.0048	-0.0324	0.0124	-0.0075	0.0252	0.0187	0.0368	-0.0051	-0.0032	0.0735	-0.0154	0.0328	36.2472	0.1339	146.2478
7	1.1573	0.397	0.3119	0.2161	0.0101	1.03	0.0214	-0.1225	0.0471	-0.003	-0.0279	0.0423	-0.0237	-0.0394	0.0066	0.0151	0.0039	-0.0029	0.0744	-0.0318	0.0311	30.249	2.0147	151.5123
8	0.194	0.2522	0.1463	1.5678	1.0328	0.6928	-0.0671	0.0723	-0.0228	-0.0692	0.0936	-0.0658	-0.0534	0.0685	-0.0265	0.0676	-0.0189	-0.0176	0.0998	0.0061	0.0232	27.9172	-4.7036	112.6502
9	0.4687	-0.3866	0.27	1.4012	-0.3654	0.2697	-0.0481	-0.0192	0.068	0.0097	0.0136	-0.128	0.0162	0.0019	0.0346	0.0349	-0.0018	-0.0118	0.077	0.0096	0.0198	26.5558	-3.76	106.3831
10	0.3558	-0.0583	0.3822	0.722	-0.0125	0.4207	-0.0734	-0.0982	0.0338	0.0687	0.0345	-0.0388	-0.0676	-0.1193	0.0389	0.0493	0.0179	-0.0085	0.0925	-0.008	0.0184	13.8809	5.4887	108.0029
11	0.5096	-0.3689	0.0695	0.9535	-0.2157	4.5657	0.0494	0.0159	-0.0907	-0.0709	0.0039	0.0816	0.1608	-0.0817	-0.0533	0.0417	-0.0279	-0.0143	0.0319	0.0089	0.0359	12.1054	-17.5742	95.9493
12	0.3285	0.1092	0.2747	0.4714	-0.2996	1.1759	0.0015	-0.1021	0.0094	0.0684	0.0383	0.0451	-0.0105	-0.2497	-0.0399	0.0176	0.016	0.0074	0.1194	0.0129	0.0054	6.7846	-1.4139	108.4942
13	0.6366	-0.3963	0.1234	0.5789	0.2272	0.3198	0.0149	0.0134	0.0169	-0.0119	-0.0239	-0.0221	-0.0062	-0.0398	0.009	0.0296	0.0016	-0.0022	0.087	0.0181	0.0322	13.9919	0.1564	93.8652
14	1.0497	-0.3854	0.2557	0.2775	-0.1992	1.0649	0.0103	0.135	0.0637	-0.0166	-0.0389	-0.067	-0.0173	0.0461	0.0286	0.0119	-0.008	-0.0002	0.0772	0.0361	0.0358	20.019	2.0442	88.624

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 36
2	X-RAY DIFFRACTION	2	A	37 - 72
3	X-RAY DIFFRACTION	3	A	73 - 115
4	X-RAY DIFFRACTION	4	A	116 - 145
5	X-RAY DIFFRACTION	5	A	146 - 182
6	X-RAY DIFFRACTION	6	A	183 - 223
7	X-RAY DIFFRACTION	7	A	224 - 253
8	X-RAY DIFFRACTION	8	B	4 - 36
9	X-RAY DIFFRACTION	9	B	37 - 72
10	X-RAY DIFFRACTION	10	B	73 - 115
11	X-RAY DIFFRACTION	11	B	116 - 145
12	X-RAY DIFFRACTION	12	B	146 - 182
13	X-RAY DIFFRACTION	13	B	183 - 223
14	X-RAY DIFFRACTION	14	B	224 - 253

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