PDB-4x7z: MycF mycinamicin III 3'-O-methyltransferase (E35Q, M56A, E139A va...

ID or keywords:

Entry

Database: PDB / ID: 4x7z

Title

MycF mycinamicin III 3'-O-methyltransferase (E35Q, M56A, E139A variant) in complex with Mg, SAH and mycinamicin III (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: 1.44 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4x7z.cif.gz	233.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4x7z.ent.gz	184.7 KB	Display	PDB format
PDBx/mmJSON format	4x7z.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4x7z_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4x7z_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4x7z_validation.xml.gz	29 KB	Display
Data in CIF	4x7z_validation.cif.gz	45 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7z ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7z	HTTPS FTP

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Related structure data

Related structure data	4x7uC 4x7vC 4x7wC 4x7xC 4x7yC 4x81C 4xvyC 4xvzC C: citing same article (ref.)
Similar structure data	4x81-d 4x7v-d 4x7u-d 2arx-d 4x7x-d 3dl0-d 1ezi-d 2phw-d 4qbh-d 4x7w-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

Deposited unit

A: Mycinamicin III 3''-O-methyltransferase

B: Mycinamicin III 3''-O-methyltransferase

hetero molecules

63.8 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)	50.354, 92.516, 127.798
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, 790 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-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-ZM3 / MYCINAMICIN III Mass: 681.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₆H₅₉NO₁₁
#5: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.42 Å³/Da / Density % sol: 49.26 %
Crystal grow	Temperature: 293.1 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20-30% PEG 5000 MME, 100 mM ammonium acetate, 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: 1.44→74.94 Å / Num. obs: 107004 / % possible obs: 99 % / Redundancy: 5.8 % / Net I/σ(I): 11.6
Reflection shell	Resolution: 1.44→1.53 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.561 / Mean I/σ(I) obs: 1.4 / % possible all: 93.6

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Processing

Software

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

Refinement

Resolution: 1.44→46.85 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.974 / SU B: 1.825 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16765	5309	5 %	RANDOM
R_work	0.15318	-	-	-
obs	0.15389	101687	98.97 %	-

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: 15.363 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.23 Å²	-0 Å²	0 Å²
2-	-	0.15 Å²	-0 Å²
3-	-	-	0.07 Å²

Refinement step

Cycle: 1 / Resolution: 1.44→46.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3963	0	161	779	4903

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	4279
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3939
X-RAY DIFFRACTION	r_angle_refined_deg	1.43	1.959	5832
X-RAY DIFFRACTION	r_angle_other_deg	0.841	3	9035
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.936	5	513
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.3	23.081	211
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.869	15	646
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.891	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	646
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	4887
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1025
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	0.61	0.852	2043
X-RAY DIFFRACTION	r_mcbond_other	0.61	0.852	2042
X-RAY DIFFRACTION	r_mcangle_it	0.984	1.275	2559
X-RAY DIFFRACTION	r_mcangle_other	0.984	1.275	2560
X-RAY DIFFRACTION	r_scbond_it	1.238	1.067	2236
X-RAY DIFFRACTION	r_scbond_other	1.238	1.068	2237
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.948	1.548	3274
X-RAY DIFFRACTION	r_long_range_B_refined	6.793	10.219	5746
X-RAY DIFFRACTION	r_long_range_B_other	6.792	10.223	5747
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.44→1.48 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.324	369	-
R_work	0.325	6496	-
obs	-	-	87.16 %

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	0.3338	-0.1621	-0.281	1.8155	-0.8879	1.0498	-0.0004	0.0454	-0.0231	-0.0944	0.0074	0.0919	0.0463	-0.1113	-0.007	0.0513	0.0006	0.0053	0.0891	-0.0045	0.0101	47.5443	97.2622	63.9704
2	0.5666	-0.477	-0.2444	1.7611	0.3756	0.6753	-0.0287	-0.0268	-0.0642	0.0107	0.0083	0.1174	-0.0183	-0.0462	0.0203	0.0261	0.0036	0.0077	0.0777	0.0004	0.0116	48.8822	96.3453	57.7471
3	0.5726	0.1491	-0.1922	0.9365	0.2102	0.6043	-0.0461	-0.0676	-0.0553	0.1052	0.0043	0.0076	0.0814	0.0835	0.0418	0.0364	0.0134	0.0074	0.0663	0.0107	0.0066	61.4992	87.0651	59.3105
4	0.719	0.1425	-0.6244	0.9122	-0.7213	2.6201	0.0371	-0.0422	0.0474	0.0127	-0.015	-0.0279	-0.0631	-0.0255	-0.0221	0.0268	-0.0166	0.0049	0.0315	-0.0043	0.016	63.3308	110.301	47.4349
5	0.5903	0.1056	-0.3498	0.75	0.2965	1.3033	-0.0121	-0.1104	-0.0134	0.089	0.0283	-0.061	0.028	0.2059	-0.0162	0.014	0.0119	-0.0084	0.1058	0.0002	0.0068	68.5858	94.0043	59.8237
6	0.7873	-0.4754	-0.0976	0.8842	-0.1779	0.4941	0.0068	0.0358	-0.001	-0.012	-0.0183	-0.0202	0.0109	0.0242	0.0115	0.0224	-0.0024	0.0013	0.0629	-0.0089	0.0098	61.4795	92.5147	45.2105
7	1.163	-0.281	-0.2701	0.5258	0.1165	1.0617	0.0015	0.0939	-0.0587	-0.0159	-0.014	0.0153	0.025	-0.0285	0.0125	0.0048	-0.0083	0.001	0.0601	-0.0173	0.0116	55.4905	90.6445	39.9402
8	0.2824	-0.205	-0.1864	2.1168	1.122	0.8574	-0.0563	-0.0199	0.009	0.0628	0.0793	-0.1345	0.086	0.0792	-0.023	0.0463	0.008	0.0083	0.0903	0.0045	0.0184	53.0811	97.1463	78.8745
9	0.5087	0.3945	-0.1983	1.8788	-0.3375	0.4499	-0.0274	0.0383	-0.0611	-0.0058	0.008	-0.1293	0.0053	0.0051	0.0194	0.0184	0.0015	0.0062	0.0758	0.0022	0.0134	51.741	96.187	85.0852
10	0.5529	-0.1001	-0.2395	0.8395	-0.1155	0.6066	-0.0448	0.0672	-0.0581	-0.1014	0.0179	-0.0034	0.0876	-0.0778	0.0269	0.0383	-0.0166	0.0023	0.0689	-0.0065	0.0075	39.0701	86.952	83.4778
11	0.6781	0.1865	-0.2516	0.9806	-0.4561	4.1343	0.0411	-0.0134	0.0847	0.0738	0.0019	0.0611	-0.1447	-0.0755	-0.043	0.0225	0.0185	0.0074	0.0255	0.0013	0.0172	37.3436	110.077	95.6224
12	0.5184	-0.0675	-0.2373	0.6662	-0.2996	1.1775	0.0007	0.1156	-0.0117	-0.0777	0.0379	0.0593	0.0439	-0.1909	-0.0387	0.0146	-0.0166	-0.01	0.1007	0.0052	0.0078	31.9714	93.8796	83.0171
13	0.7293	0.424	-0.1348	0.7731	0.1647	0.5655	0.0017	-0.0309	-0.0088	0.007	-0.0048	0.0151	0.0121	-0.0201	0.0031	0.0193	-0.0003	-0.0045	0.0688	0.0139	0.0082	39.1895	92.2462	97.6556
14	1.2086	0.17	-0.362	0.581	-0.2227	1.1482	0.0121	-0.1306	-0.0778	0.0196	-0.017	-0.0349	0.0304	0.0553	0.0049	0.0053	0.0027	-0.0058	0.0631	0.0211	0.0163	45.0955	90.1003	102.9139

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 - 254

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