PDB-4x7v: MycF mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant)...

ID or keywords:

Entry

Database: PDB / ID: 4x7v

Title

MycF mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex with Mg, SAH and mycinamicin IV (product)

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: 1.45 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	Nov 22, 2017	Group: Derived calculations / Refinement description / Source and taxonomy Category: entity_src_gen / pdbx_struct_oper_list / software Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	4x7v.cif.gz	239.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4x7v.ent.gz	189.9 KB	Display	PDB format
PDBx/mmJSON format	4x7v.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x7v_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4x7v_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4x7v_validation.xml.gz	30.8 KB	Display
Data in CIF	4x7v_validation.cif.gz	46.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7v ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7v	HTTPS FTP

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Related structure data

Related structure data	4x7uC 4x7wC 4x7xC 4x7yC 4x7zC 4x81C 4xvyC 4xvzC C: citing same article (ref.)
Similar structure data	4x7z-d 4x7x-d 4x81-d 3oqi-d 3s7t-d 4iuo-d 1ezi-d 4mg4-4 2wk1-1 1lgc-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: Mycinamicin III 3''-O-methyltransferase

B: Mycinamicin III 3''-O-methyltransferase

hetero molecules

63.7 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)	50.133, 92.544, 128.540
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Mycinamicin III 3''-O-methyltransferase / Mycinamicin biosynthesis protein F Mass: 30757.541 Da / Num. of mol.: 2 / Mutation: E35Q, 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
#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-MIV / MYCINAMICIN IV Mass: 695.880 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₇H₆₁NO₁₁
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 789 / 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: 49.25 %
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: 1.0332 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 13, 2012
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: 1.45→50 Å / Num. obs: 99022 / % possible obs: 92.4 % / Redundancy: 6.7 % / Net I/σ(I): 19.2

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1593)	refinement
XDS		data scaling
Aimless		data scaling
Coot		model building
PHASER		phasing

Refinement

Resolution: 1.45→44.081 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.177	4928	4.98 %	Random selection
R_work	0.1613	-	-	-
obs	0.1621	98896	92.7 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.45→44.081 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3988	0	152	789	4929

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4356
X-RAY DIFFRACTION	f_angle_d	1.379	5943
X-RAY DIFFRACTION	f_dihedral_angle_d	11.17	1575
X-RAY DIFFRACTION	f_chiral_restr	0.054	653
X-RAY DIFFRACTION	f_plane_restr	0.01	777

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.45-1.4665	0.2054	97	0.2112	1895	X-RAY DIFFRACTION	56
1.4665-1.4837	0.2075	103	0.2083	2045	X-RAY DIFFRACTION	61
1.4837-1.5018	0.256	102	0.1991	2165	X-RAY DIFFRACTION	65
1.5018-1.5208	0.2153	122	0.1983	2365	X-RAY DIFFRACTION	70
1.5208-1.5409	0.2582	136	0.1895	2489	X-RAY DIFFRACTION	76
1.5409-1.562	0.2306	126	0.1809	2702	X-RAY DIFFRACTION	80
1.562-1.5843	0.2045	153	0.1786	2875	X-RAY DIFFRACTION	86
1.5843-1.6079	0.2074	181	0.1805	3037	X-RAY DIFFRACTION	92
1.6079-1.6331	0.1775	197	0.1703	3234	X-RAY DIFFRACTION	97
1.6331-1.6598	0.1763	176	0.1701	3332	X-RAY DIFFRACTION	100
1.6598-1.6885	0.1596	158	0.1659	3334	X-RAY DIFFRACTION	100
1.6885-1.7192	0.199	175	0.1668	3351	X-RAY DIFFRACTION	100
1.7192-1.7522	0.1754	165	0.1649	3369	X-RAY DIFFRACTION	100
1.7522-1.788	0.2022	181	0.1626	3330	X-RAY DIFFRACTION	100
1.788-1.8269	0.175	186	0.1627	3311	X-RAY DIFFRACTION	100
1.8269-1.8694	0.1709	162	0.1582	3388	X-RAY DIFFRACTION	100
1.8694-1.9161	0.1725	187	0.1652	3364	X-RAY DIFFRACTION	100
1.9161-1.9679	0.1851	183	0.1671	3329	X-RAY DIFFRACTION	100
1.9679-2.0258	0.2062	165	0.1671	3400	X-RAY DIFFRACTION	100
2.0258-2.0912	0.1708	175	0.1635	3364	X-RAY DIFFRACTION	100
2.0912-2.166	0.1747	177	0.1551	3366	X-RAY DIFFRACTION	100
2.166-2.2527	0.1679	178	0.1618	3364	X-RAY DIFFRACTION	100
2.2527-2.3552	0.1819	174	0.1561	3395	X-RAY DIFFRACTION	100
2.3552-2.4794	0.164	188	0.1617	3388	X-RAY DIFFRACTION	100
2.4794-2.6347	0.1846	189	0.1685	3406	X-RAY DIFFRACTION	100
2.6347-2.8381	0.1785	168	0.1672	3404	X-RAY DIFFRACTION	100
2.8381-3.1236	0.1888	191	0.1628	3420	X-RAY DIFFRACTION	100
3.1236-3.5754	0.1763	167	0.1541	3451	X-RAY DIFFRACTION	100
3.5754-4.504	0.1542	194	0.1385	3464	X-RAY DIFFRACTION	100
4.504-44.1009	0.1496	172	0.1544	3631	X-RAY DIFFRACTION	99

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	1.1371	-0.6693	-0.5032	4.0584	-1.0335	2.154	0.0216	0.1194	0.0107	-0.092	0.0058	0.2903	0.0004	-0.1958	-0.0717	0.0975	-0.0002	0.0098	0.1493	-0.0088	0.0839	47.0007	5.0024	-64.0386
2	0.8025	-0.8407	-0.2651	3.4325	0.8521	1.3146	-0.005	0.0134	-0.0601	-0.0099	-0.0619	0.2675	-0.0656	-0.1881	0.0619	0.1138	-0.0046	0.0208	0.1537	0.0077	0.1144	48.1262	4.0557	-70.6019
3	0.9745	0.0337	-0.39	2.5546	0.0817	1.2153	-0.0508	-0.0688	-0.151	0.13	-0.0167	-0.0029	0.1421	0.0602	0.0728	0.1188	0.0123	0.0071	0.106	0.0114	0.0952	61.2761	-5.117	-69.104
4	0.8415	0.0798	-1.9022	1.5441	-0.7067	9.3903	0.0948	-0.022	0.086	-0.0598	-0.0028	-0.0117	-0.0696	0.0788	-0.0961	0.117	-0.0139	0.0048	0.0838	0.0019	0.1432	63.1389	17.8162	-81.0093
5	1.8779	0.3172	-1.2603	0.9691	0.266	3.4501	-0.0418	-0.1228	-0.0944	0.1046	-0.0045	-0.1162	0.0812	0.2177	0.0443	0.0967	0.0191	-0.0244	0.1278	0.0096	0.1218	68.1713	1.3915	-68.1668
6	0.971	-0.5738	0.0729	1.1596	-0.2502	0.6263	0.013	0.0629	-0.0069	0.0224	-0.0446	0.0382	0.0048	0.0217	0.0317	0.1169	-0.002	0.0066	0.1155	-0.0057	0.1153	60.9674	0.5034	-83.2629
7	3.721	-1.2465	-1.7261	1.5914	0.6819	3.1034	-0.0365	0.1808	-0.081	-0.0318	-0.0127	0.0508	0.1107	0.0039	0.0459	0.0711	-0.009	-0.0162	0.1026	-0.025	0.0915	54.8881	-1.7516	-88.3344
8	0.7174	-0.1753	-0.3477	3.9298	1.5805	1.7901	-0.0607	-0.0436	-0.0247	0.0784	0.0788	-0.2297	0.1095	0.136	-0.0597	0.1041	0.0176	0.0128	0.1437	0.0186	0.0887	53.0529	4.86	-49.5709
9	0.9924	1.06	-0.2195	4.2519	-1.1884	1.1278	-0.0408	0.005	-0.1209	-0.0156	-0.0548	-0.3037	0.0119	0.107	0.1076	0.1061	0.0171	0.017	0.1312	0.0084	0.1122	51.7689	3.6143	-42.8081
10	1.2533	-0.1914	-0.5193	2.5356	-0.2362	1.4115	-0.0789	0.0896	-0.183	-0.1342	-0.0159	0.0308	0.1859	-0.109	0.092	0.1101	-0.019	0.0066	0.1061	-0.0043	0.0974	38.7531	-5.2577	-44.5726
11	1.4641	0.2294	-0.8093	2.1437	-0.9595	2.2133	0.0201	-0.0881	0.121	0.2555	0.0561	0.1068	-0.209	-0.1452	-0.1109	0.1483	0.0268	0.0065	0.1324	0.0141	0.1456	37.1678	17.5016	-32.1782
12	1.7415	-0.1927	-1.2187	0.6226	-0.3719	2.9999	-0.0531	0.1607	-0.1126	-0.0781	0.0285	0.051	0.1238	-0.2624	0.0166	0.1041	-0.0231	-0.0201	0.1551	0.0008	0.1255	31.6793	0.9698	-45.3014
13	0.9314	0.5027	-0.1306	0.8631	0.0021	0.7065	-0.002	-0.06	-0.0579	-0.0261	-0.0272	-0.0528	0.0042	-0.0583	0.0284	0.1135	0.0012	0.0041	0.1186	0.0211	0.1159	39.2637	0.1487	-30.2877
14	3.0972	0.352	-1.2133	0.9616	-0.5185	3.0417	-0.0256	-0.2861	-0.1722	0.0006	-0.0268	-0.0758	0.0793	0.0581	0.0565	0.0812	0.0077	-0.0169	0.1229	0.042	0.1257	44.706	-2.2351	-24.5643

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:36)
2	X-RAY DIFFRACTION	2	(chain A and resid 37:72)
3	X-RAY DIFFRACTION	3	(chain A and resid 73:115)
4	X-RAY DIFFRACTION	4	(chain A and resid 116:145)
5	X-RAY DIFFRACTION	5	(chain A and resid 146:182)
6	X-RAY DIFFRACTION	6	(chain A and resid 183:223)
7	X-RAY DIFFRACTION	7	(chain A and resid 224:254)
8	X-RAY DIFFRACTION	8	(chain B and resid 3:36)
9	X-RAY DIFFRACTION	9	(chain B and resid 37:72)
10	X-RAY DIFFRACTION	10	(chain B and resid 73:115)
11	X-RAY DIFFRACTION	11	(chain B and resid 116:145)
12	X-RAY DIFFRACTION	12	(chain B and resid 146:182)
13	X-RAY DIFFRACTION	13	(chain B and resid 183:223)
14	X-RAY DIFFRACTION	14	(chain B and resid 224:254)

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