PDB-4x7u: MycF mycinamicin III 3'-O-methyltransferase in complex with Mg, S...

ID or keywords:

Entry

Database: PDB / ID: 4x7u

Title

MycF mycinamicin III 3'-O-methyltransferase 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 /

MOLECULAR REPLACEMENT / Resolution: 1.65 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	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / refine_hist / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _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 / _refine_hist.d_res_low / _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	4x7u.cif.gz	230.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4x7u.ent.gz	183.2 KB	Display	PDB format
PDBx/mmJSON format	4x7u.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4x7u_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4x7u_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4x7u_validation.xml.gz	26.7 KB	Display
Data in CIF	4x7u_validation.cif.gz	39.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x7/4x7u ftp://data.pdbj.org/pub/pdb/validation_reports/x7/4x7u	HTTPS FTP

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Related structure data

Related structure data	4x7vC 4x7wC 4x7xC 4x7yC 4x7zC 4x81C 4xvySC 4xvzC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4x81-d 4x7w-d 4x7z-d 3oqh-d 2arx-d 4x7y-d 2ar6-d 4q1e-d 4isr-2 4xvy-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)	49.856, 90.850, 128.641
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Mycinamicin III 3''-O-methyltransferase / Mycinamicin biosynthesis protein F Mass: 30816.561 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora griseorubida (bacteria) / Gene: mycF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q49492, mycinamicin III 3''-O-methyltransferase
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#4: Chemical	ChemComp-ZM3 / MYCINAMICIN III Mass: 681.854 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃₆H₅₉NO₁₁
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.36 Å³/Da / Density % sol: 47.96 %
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-B / Wavelength: 1.033 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2012
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: 1.65→50 Å / Num. obs: 71066 / % possible obs: 99.4 % / Redundancy: 3.6 % / R_sym value: 0.073 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.1 / R_sym value: 0.588 / % possible all: 99.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0073	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4XVY

4xvy

Resolution: 1.65→43.71 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.966 / SU B: 3.244 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.079 / 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	0.16788	3571	5.1 %	RANDOM
R_work	0.14786	-	-	-
obs	0.14886	67012	99.32 %	-

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: 18.255 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.42 Å²	0 Å²	0 Å²
2-	-	1.41 Å²	0 Å²
3-	-	-	-1 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→43.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3996	0	150	572	4718

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.019	4360
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3986
X-RAY DIFFRACTION	r_angle_refined_deg	1.28	1.959	5949
X-RAY DIFFRACTION	r_angle_other_deg	0.804	3	9164
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.838	5	526
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.907	23.333	219
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.458	15	666
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.543	15	40
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	652
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5010
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1038
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	0.66	1.129	2080
X-RAY DIFFRACTION	r_mcbond_other	0.66	1.129	2079
X-RAY DIFFRACTION	r_mcangle_it	1.125	1.686	2614
X-RAY DIFFRACTION	r_mcangle_other	1.125	1.686	2615
X-RAY DIFFRACTION	r_scbond_it	1.106	1.372	2280
X-RAY DIFFRACTION	r_scbond_other	1.106	1.372	2281
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.843	2.008	3336
X-RAY DIFFRACTION	r_long_range_B_refined	6.114	11.486	5504
X-RAY DIFFRACTION	r_long_range_B_other	5.505	10.234	5176
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.238	251	-
R_work	0.239	4799	-
obs	-	-	97.91 %

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	0.182	-0.0948	-0.0481	1.7101	-0.8041	0.5064	0.0045	0.013	-0.0085	-0.097	-0.0223	0.0505	0.0303	-0.0725	0.0178	0.0607	0.027	0.0008	0.0781	-0.0353	0.0218	-15.7254	-18.9961	44.6428
2	0.3803	-0.5232	-0.1542	1.266	0.5169	0.6557	-0.0465	-0.0672	-0.0498	-0.0286	0.0047	0.0909	-0.0363	-0.0191	0.0419	0.0407	0.0177	0.0043	0.0532	-0.0181	0.0281	-14.087	-18.9145	38.0585
3	0.1415	0.0323	-0.1385	0.6104	0.0341	0.398	-0.0712	-0.0648	0.0199	0.0662	0.0711	0.051	0.0682	0.1693	0	0.0495	0.0378	-0.0001	0.0825	-0.0041	0.0185	-1.6324	-28.4041	39.4194
4	0.5759	0.5713	-0.4801	1.4314	-0.3224	2.6258	-0.0753	-0.0707	0.1573	-0.1297	0.1221	-0.1027	-0.1893	0.1427	-0.0468	0.0542	-0.0139	-0.0165	0.0546	-0.0747	0.1285	0.5229	-4.6984	28.9857
5	0.6947	0.0369	-0.3922	0.6913	0.2326	1.1399	-0.0291	-0.108	0.0497	0.0952	0.06	-0.073	0.0324	0.2907	-0.031	0.0168	0.0162	-0.0162	0.1076	-0.0224	0.0183	5.673	-21.6665	40.441
6	0.5284	-0.3703	-0.0038	0.4119	-0.2022	0.5805	0.0039	0.0121	0.0186	-0.0064	-0.0088	0.0267	-0.0048	0.0958	0.0049	0.0292	0.0017	0.0009	0.0678	-0.0079	0.0411	-1.4031	-22.2039	25.5369
7	1.0824	-0.2168	0.2192	0.194	0.2341	0.8842	0.0119	0.108	-0.0083	0.0005	0.0064	0.0363	0.0179	0.0163	-0.0183	0.0238	-0.0001	0.0027	0.053	-0.0035	0.0482	-7.2371	-24.0896	20.074
8	0.0196	0.1689	0.0897	1.9999	1.1327	0.8702	-0.0025	0.0058	0.0011	0.1145	0.0253	-0.0457	0.0825	0.1157	-0.0227	0.0605	0.0132	0.0059	0.0654	0.001	0.0287	-9.9489	-19.4141	59.033
9	0.4013	0.4299	-0.3408	1.7025	-0.4536	0.3059	-0.0169	0.0203	-0.0559	-0.0075	-0.0199	-0.1196	-0.0038	-0.0091	0.0368	0.0495	0.0049	0.0048	0.0326	-0.0028	0.0478	-11.2831	-19.9651	65.4318
10	0.2502	-0.1191	-0.2823	0.8326	-0.107	0.3961	-0.0298	0.0659	-0.0361	-0.0577	-0.0101	0.0197	0.0433	-0.08	0.0398	0.0589	-0.009	-0.0033	0.0351	-0.0219	0.0459	-23.8907	-29.1432	63.9325
11	0.1231	0.0277	-0.237	0.8635	-0.0805	3.2893	0.0689	0.0469	0.0258	0.0855	-0.0144	0.0411	-0.1442	-0.0864	-0.0545	0.0594	0.0162	0.0148	0.0229	0.0063	0.0442	-25.3869	-6.0579	75.9329
12	0.2425	-0.1877	-0.3559	0.6129	-0.2441	1.1647	0.0247	0.0846	-0.0234	-0.0459	0.0102	0.0621	0.0077	-0.1752	-0.035	0.0214	-0.003	-0.0167	0.068	-0.0092	0.0297	-30.9707	-22.2548	63.5712
13	0.4799	0.275	-0.2611	0.6499	0.2638	0.5087	-0.0059	-0.0132	-0.0235	0.0155	-0.0161	0.0162	0.0062	0.0273	0.0219	0.0369	-0.0004	-0.0041	0.0463	0.002	0.0535	-23.5384	-23.8229	78.147
14	0.9081	0.195	-0.4932	0.3568	-0.0649	1.2049	-0.0348	-0.1489	-0.0593	0.0253	-0.0033	-0.0053	0.0327	0.1454	0.0381	0.0158	0.0127	-0.0063	0.0423	0.0236	0.0506	-17.5577	-26.0104	83.3113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 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 - 254
8	X-RAY DIFFRACTION	8	B	3 - 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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