PDB-4xvz: MycF mycinamicin III 3'-O-methyltransferase in complex with Mg

ID or keywords:

Entry

Database: PDB / ID: 4xvz

Title

MycF mycinamicin III 3'-O-methyltransferase in complex with Mg

Components

Mycinamicin III 3''-O-methyltransferase

Keywords

TRANSFERASE / macrolide / methyltransferase / antibiotic / natural product

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 /

SAD / Resolution: 2.49 Å

Authors

Akey, D.L. / 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	Jan 28, 2015	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	Oct 23, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / refine_hist / struct_conn / struct_ncs_dom_lim 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xvz.cif.gz	335.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4xvz.ent.gz	273.8 KB	Display	PDB format
PDBx/mmJSON format	4xvz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4xvz_validation.pdf.gz	472.4 KB	Display	wwPDB validaton report
Full document	4xvz_full_validation.pdf.gz	482.7 KB	Display
Data in XML	4xvz_validation.xml.gz	35.4 KB	Display
Data in CIF	4xvz_validation.cif.gz	45.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xv/4xvz ftp://data.pdbj.org/pub/pdb/validation_reports/xv/4xvz	HTTPS FTP

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Related structure data

Related structure data	4x7uC 4x7vC 4x7wC 4x7xC 4x7yC 4x7zC 4x81C 4xvyC C: citing same article (ref.)
Similar structure data	3wb8-8 4co6-1 5i10-2 3cm3-1 3rog-2 2xvo-2 4oyh-2 1yem-d 4zxs-1 3pg2-1 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: Mycinamicin III 3''-O-methyltransferase

B: Mycinamicin III 3''-O-methyltransferase

C: Mycinamicin III 3''-O-methyltransferase

D: Mycinamicin III 3''-O-methyltransferase

hetero molecules

129 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Mycinamicin III 3''-O-methyltransferase

B: Mycinamicin III 3''-O-methyltransferase

hetero molecules

defined by author&software
64.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Mycinamicin III 3''-O-methyltransferase

D: Mycinamicin III 3''-O-methyltransferase

hetero molecules

defined by software
64.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	123.864, 148.587, 66.855
Angle α, β, γ (deg.)	90.00, 120.23, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	ARG	ARG	A	A	2 - 252	25 - 275
2	1	SER	SER	ARG	ARG	B	B	2 - 252	25 - 275
1	2	SER	SER	ASN	ASN	A	A	2 - 256	25 - 279
2	2	SER	SER	ASN	ASN	C	C	2 - 256	25 - 279
1	3	SER	SER	SER	SER	A	A	2 - 253	25 - 276
2	3	SER	SER	SER	SER	D	D	2 - 253	25 - 276
1	4	ALA	ALA	ARG	ARG	B	B	1 - 252	24 - 275
2	4	ALA	ALA	ARG	ARG	C	C	1 - 252	24 - 275
1	5	SER	SER	SER	SER	B	B	2 - 253	25 - 276
2	5	SER	SER	SER	SER	D	D	2 - 253	25 - 276
1	6	SER	SER	SER	SER	C	C	2 - 253	25 - 276
2	6	SER	SER	SER	SER	D	D	2 - 253	25 - 276

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Mycinamicin III 3''-O-methyltransferase / Mycinamicin biosynthesis protein F Mass: 32164.662 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycF / Plasmid: pMCSG7-mycF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.54 %
Crystal grow	Temperature: 293.1 K / Method: vapor diffusion / Details: 20-30% PEG 3350, 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: 0.97944 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2010
Radiation	Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97944 Å / Relative weight: 1
Reflection	Resolution: 2.49→86.85 Å / Num. obs: 36246 / % possible obs: 100 % / Redundancy: 5.8 % / R_sym value: 0.08 / Net I/σ(I): 13.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
HKL-2000		data reduction
DENZO		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.49→45.6 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.946 / SU B: 16.63 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21695	1811	5 %	RANDOM
R_work	0.17828	-	-	-
obs	0.18014	34422	99.31 %	-

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: 60.453 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.18 Å²	0 Å²	1.46 Å²
2-	-	-1.49 Å²	0 Å²
3-	-	-	-1.42 Å²

Refinement step

Cycle: 1 / Resolution: 2.49→45.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6315	0	8	135	6458

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	6455
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	6027
X-RAY DIFFRACTION	r_angle_refined_deg	1.701	1.955	8752
X-RAY DIFFRACTION	r_angle_other_deg	1.218	3	13763
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.047	5	787
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.021	22.268	313
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.492	15	967
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.001	15	69
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	957
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	7316
X-RAY DIFFRACTION	r_gen_planes_other	0.007	0.02	1589
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	3.201	3.622	3184
X-RAY DIFFRACTION	r_mcbond_other	3.201	3.621	3183
X-RAY DIFFRACTION	r_mcangle_it	5.01	5.4	3959
X-RAY DIFFRACTION	r_mcangle_other	5.009	5.401	3960
X-RAY DIFFRACTION	r_scbond_it	4.177	4.165	3271
X-RAY DIFFRACTION	r_scbond_other	4.176	4.166	3272
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.591	6.077	4794
X-RAY DIFFRACTION	r_long_range_B_refined	9.031	30.124	7422
X-RAY DIFFRACTION	r_long_range_B_other	9.024	30.065	7389
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	11943	0.06
1	2	B	11943	0.06
2	1	A	12050	0.07
2	2	C	12050	0.07
3	1	A	11933	0.07
3	2	D	11933	0.07
4	1	B	11777	0.08
4	2	C	11777	0.08
5	1	B	11865	0.07
5	2	D	11865	0.07
6	1	C	11847	0.07
6	2	D	11847	0.07

LS refinement shell

Resolution: 2.49→2.555 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	117	-
R_work	0.284	2304	-
obs	-	-	91.02 %

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	0.3193	-0.1973	0.2321	2.1973	0.69	0.5184	-0.0255	-0.0187	0.016	-0.1744	0.0246	-0.0217	-0.0954	0.0449	0.0009	0.2331	-0.0506	-0.0065	0.1935	-0.0418	0.2931	9.1264	75.2294	19.7962
2	1.2577	0.039	0.9802	0.7841	-0.2824	1.037	-0.0253	-0.0794	0.1677	0.0581	0.0165	0.2205	-0.0513	0.0699	0.0088	0.2191	-0.0264	0.0283	0.1765	-0.0514	0.2697	0.0808	65.2395	23.8604
3	0.7532	-0.1459	0.1549	0.9778	0.3902	0.5757	0.0637	-0.1568	0.0237	0.1502	-0.0935	-0.0038	0.0945	-0.0633	0.0299	0.2545	-0.0481	0.0199	0.2086	-0.0158	0.2031	4.8854	58.4662	29.5567
4	1.412	-0.1636	-0.0716	1.5732	0.5509	0.2301	0.105	0.0797	-0.1097	0.0863	-0.0475	0.0093	0.0451	0.0448	-0.0574	0.2242	-0.0217	-0.0172	0.1872	-0.0082	0.2604	10.2504	49.6181	16.4234
5	0.675	0.5318	0.5386	3.9447	0.2919	0.4402	-0.0693	0.0447	0.2031	0.1325	-0.0679	0.4118	-0.0604	0.0665	0.1372	0.2516	-0.0378	-0.0167	0.1493	-0.1018	0.3219	1.3065	87.9094	26.8644
6	3.1025	0.9857	0.6466	1.92	1.3042	0.9981	-0.2655	-0.1089	0.3112	-0.3476	0.0483	0.4174	-0.0859	0.0826	0.2172	0.3908	-0.0368	-0.1901	0.1002	-0.0205	0.3476	2.1618	97.0842	16.1632
7	1.3857	1.071	0.1877	3.2622	0.9877	0.6471	-0.2912	-0.0132	0.1807	-0.4999	0.1204	0.2629	-0.3244	0.205	0.1708	0.3451	-0.1121	-0.1351	0.0995	0.0061	0.2666	7.2604	105.2539	19.1577
8	0.6134	-0.07	-0.5802	3.3752	1.9463	1.602	0.0953	-0.2175	0.2928	-0.0238	-0.4524	1.051	-0.1239	-0.0617	0.3572	0.2537	-0.0337	-0.1778	0.1457	-0.2546	0.6931	-5.2984	111.6042	27.6158
9	0.1826	0.131	0.0037	1.8794	-0.727	0.3021	-0.0594	0.0301	0.0189	-0.1231	0.0413	-0.0347	0.0382	-0.0345	0.0181	0.2676	-0.0424	0.0118	0.1871	-0.0024	0.2593	8.2968	108.1569	57.2797
10	1.3435	-0.5361	0.91	0.7776	-0.0333	0.8274	0.0453	-0.0342	-0.074	0.2515	0.0194	-0.0259	0.1686	-0.0691	-0.0647	0.2505	-0.0343	0.0059	0.2124	0.0016	0.2278	8.2298	118.2633	67.0884
11	0.6538	-0.0436	0.1461	1.1055	-0.2314	0.597	0.0309	-0.0937	0.0824	0.1012	-0.0552	0.1243	-0.0128	-0.0842	0.0243	0.2133	-0.0187	0.0377	0.2234	-0.0276	0.2194	1.5566	125.1285	65.7445
12	0.24	-0.4732	0.4748	1.0861	-1.0065	0.9739	-0.0697	0.0378	0.058	0.0796	0.0316	0.0205	-0.1149	0.0419	0.0381	0.2244	-0.0201	-0.0184	0.1988	-0.0075	0.2701	10.3142	133.4	54.7836
13	0.0619	-0.0295	0	2.0849	0.1236	0.0079	0.0197	0.0461	-0.0637	0.3678	-0.0245	0.1108	0.0307	-0.0077	0.0048	0.274	-0.0721	0.0007	0.161	0.0202	0.2892	4.5909	95.6584	67.5166
14	2.6649	1.4568	0.5271	1.5148	-0.2538	1.0299	0.0956	-0.081	-0.2063	-0.0195	0.0153	-0.4226	-0.0212	-0.2509	-0.1109	0.2479	-0.0316	0.0063	0.1329	0.0446	0.4301	14.088	86.1665	61.9291
15	0.9278	1.0232	0.1346	2.3417	0.542	0.782	0.0127	0.1417	-0.3193	-0.0242	0.099	-0.2632	0.0373	-0.0978	-0.1117	0.2081	-0.0831	-0.0381	0.0954	-0.0345	0.3234	8.8527	77.8286	59.3538
16	0.9012	1.5733	-0.8105	2.7533	-1.4188	0.7958	0.3473	-0.2707	-0.2665	0.6278	-0.4727	-0.4312	-0.1814	0.1503	0.1253	0.487	-0.2755	-0.2725	0.2361	0.1933	0.4367	8.4714	71.5775	74.2491

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 66
2	X-RAY DIFFRACTION	2	A	67 - 115
3	X-RAY DIFFRACTION	3	A	145 - 223
4	X-RAY DIFFRACTION	4	A	224 - 257
5	X-RAY DIFFRACTION	5	B	1 - 66
6	X-RAY DIFFRACTION	6	B	67 - 115
7	X-RAY DIFFRACTION	7	B	145 - 223
8	X-RAY DIFFRACTION	8	B	224 - 253
9	X-RAY DIFFRACTION	9	C	0 - 66
10	X-RAY DIFFRACTION	10	C	67 - 116
11	X-RAY DIFFRACTION	11	C	145 - 223
12	X-RAY DIFFRACTION	12	C	224 - 257
13	X-RAY DIFFRACTION	13	D	2 - 66
14	X-RAY DIFFRACTION	14	D	67 - 115
15	X-RAY DIFFRACTION	15	D	145 - 223
16	X-RAY DIFFRACTION	16	D	224 - 254

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