PDB-5n5d: Crystal Structure of the O-Methyltransferase TomG from Streptomyc...

ID or keywords:

Entry

Database: PDB / ID: 5n5d

Title

Crystal Structure of the O-Methyltransferase TomG from Streptomyces achromogenes involved in Tomaymycin synthesis in complex with SAM

Components

Methyltransferase

Keywords

TRANSFERASE / o-Methyltransferase / tomaymycin / Rossmann-like fold / S-adenosyl methionine

Function / homology

Function and homology information

O-methyltransferase activity
Similarity search - Function

Biological species

Streptomyces regensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Pippel, J. / Blankenfeldt, W.

Citation

Journal: Cell Chem Biol / Year: 2017
Title: Total Biosynthesis of the Pyrrolo[4,2]benzodiazepine Scaffold Tomaymycin on an In Vitro Reconstituted NRPS System.
Authors: von Tesmar, A. / Hoffmann, M. / Pippel, J. / Fayad, A.A. / Dausend-Werner, S. / Bauer, A. / Blankenfeldt, W. / Muller, R.

History

Deposition	Feb 13, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 1, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Aug 14, 2019	Group: Data collection / Category: reflns / reflns_shell Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rrim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rrim_I_all
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5n5d.cif.gz	280.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5n5d.ent.gz	231.2 KB	Display	PDB format
PDBx/mmJSON format	5n5d.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5n5d_validation.pdf.gz	964.6 KB	Display	wwPDB validaton report
Full document	5n5d_full_validation.pdf.gz	965.2 KB	Display
Data in XML	5n5d_validation.xml.gz	23.3 KB	Display
Data in CIF	5n5d_validation.cif.gz	35.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n5/5n5d ftp://data.pdbj.org/pub/pdb/validation_reports/n5/5n5d	HTTPS FTP

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Related structure data

Related structure data	3cbgS S: Starting model for refinement
Similar structure data	5log-d 5sup-1 3tr6-1 5kva-d 1eoc-d 2hnk-2 3cbg-1 4rvd-d 5sup-2 4pca-3 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
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Methyltransferase

B: Methyltransferase

hetero molecules

51.2 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)	67.597, 75.877, 86.784
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	Methyltransferase Mass: 24622.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces regensis (bacteria) / Gene: ACZ91_32315 / Variant: FH6421 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J8AIC3

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Non-polymers , 5 types, 502 molecules

#2: Chemical	ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL Mass: 90.121 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.26 Å³/Da / Density % sol: 45.57 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 2.1 M NH4(SO4)2, 0.1 M Li2SO4, 0.1 M Hepes pH 7.3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 1.55→50.47 Å / Num. obs: 65091 / % possible obs: 99.6 % / Redundancy: 13.2 % / CC_1/2: 1 / R_rim(I) all: 0.079 / Net I/σ(I): 22.9
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 13 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 40703 / Num. unique all: 3142 / CC_1/2: 0.783 / R_rim(I) all: 1.691 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	(dev_2608: ???)	refinement
XDS	May 1, 2016	data reduction
XDS	May 1, 2016	data scaling
Aimless	7.0.022	data scaling
PHASER	2.7.16	phasing
Coot	0.7.2.1	model building
PHENIX	dev-2650	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3cbg

3cbg

Resolution: 1.55→50.47 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.02

	R_factor	Num. reflection	% reflection
R_free	0.1661	1622	2.5 %
R_work	0.1482	-	-
obs	0.1486	65001	99.4 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.55→50.47 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3434	0	121	488	4043

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	3801
X-RAY DIFFRACTION	f_angle_d	0.715	5220
X-RAY DIFFRACTION	f_dihedral_angle_d	15.433	2323
X-RAY DIFFRACTION	f_chiral_restr	0.046	598
X-RAY DIFFRACTION	f_plane_restr	0.004	702

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 (%)
1.5501-1.5957	0.2889	137	0.2791	5131	X-RAY DIFFRACTION	99
1.5957-1.6472	0.2167	148	0.2275	5209	X-RAY DIFFRACTION	99
1.6472-1.7061	0.2525	126	0.2173	5162	X-RAY DIFFRACTION	99
1.7061-1.7744	0.1892	155	0.1775	5195	X-RAY DIFFRACTION	99
1.7744-1.8552	0.1501	141	0.1531	5216	X-RAY DIFFRACTION	99
1.8552-1.953	0.1667	125	0.1455	5272	X-RAY DIFFRACTION	100
1.953-2.0754	0.147	134	0.1363	5228	X-RAY DIFFRACTION	99
2.0754-2.2356	0.1459	130	0.1317	5298	X-RAY DIFFRACTION	100
2.2356-2.4606	0.1606	122	0.1325	5315	X-RAY DIFFRACTION	100
2.4606-2.8166	0.1467	127	0.1367	5377	X-RAY DIFFRACTION	100
2.8166-3.5485	0.1877	132	0.1364	5386	X-RAY DIFFRACTION	100
3.5485-50.4995	0.1502	145	0.1461	5590	X-RAY DIFFRACTION	100

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	1.9703	0.2727	0.0212	0.1466	-0.4559	1.9229	0.1609	0.0624	0.1834	0.1532	-0.0792	0.0667	-0.226	-0.0647	-0.0947	0.2004	0.0197	0.0382	0.1567	0.0193	0.1494	15.7069	7.5981	-34.8588
2	5.638	-3.7232	-4.5447	4.6296	6.0768	8.082	0.302	0.2923	0.4236	-0.2638	-0.1037	0.0405	-0.6726	-0.6542	0.0589	0.2406	0.064	0.0101	0.2328	0.064	0.2174	-2.4124	5.9926	-36.3198
3	2.4545	-0.6488	-0.0913	2.1289	-1.5071	3.395	0.1118	0.0915	0.0386	0.1119	-0.0998	-0.0528	0.0381	0.0236	0.014	0.1252	-0.0048	-0.014	0.1672	-0.0136	0.0917	9.4416	-6.6327	-27.3193
4	2.876	-2.7691	-1.9313	4.0291	2.4975	3.3703	0.0366	0.0542	-0.002	0.0739	-0.0572	0.1526	0.0793	-0.044	0.0408	0.0739	-0.0303	-0.0276	0.154	-0.0116	0.0952	1.478	-8.1223	-28.4682
5	5.4046	-4.3061	0.4468	4.268	-2.5942	6.0341	-0.1371	-0.1256	0.0162	0.2473	0.2398	0.3651	-0.3629	-0.5224	0.0075	0.0696	-0.0314	-0.0133	0.1868	-0.008	0.1724	-8.7216	-3.1011	-25.3943
6	0.8356	0.2492	-0.6949	1.4765	-0.7289	6.3082	0.0235	-0.0013	0.0568	0.0073	0.045	0.2513	0.1189	-0.3653	-0.0846	0.1316	-0.0376	-0.0188	0.2295	-0.006	0.2018	-7.6626	-8.8137	-25.4206
7	1.0511	0.4207	-0.0169	2.5323	0.4353	1.4773	0.048	-0.0162	-0.0869	0.0685	-0.0478	0.0695	0.0897	-0.1067	-0.0032	0.1557	-0.0082	-0.0046	0.1821	0.0022	0.1336	2.5822	-4.9905	-14.67
8	0.4125	-0.3496	0.047	0.8829	-0.187	1.5135	-0.0213	-0.0386	-0.0004	0.0496	0.0207	0.0178	-0.052	-0.0297	-0.0021	0.1546	-0.0017	-0.0084	0.1627	0.0002	0.1298	9.1929	2.6989	-10.8288
9	1.6559	0.097	0.4818	0.2187	-0.7707	3.4054	0.0727	-0.0686	0.1262	-0.0435	-0.0081	-0.0002	-0.1613	0.0808	-0.1272	0.1635	-0.004	0.0289	0.1657	-0.0206	0.127	18.7838	6.746	-8.8851
10	7.1151	3.4721	-3.7879	3.5254	-0.4721	3.6128	0.1545	-0.4383	-0.0117	0.34	-0.1461	-0.416	-0.2005	0.4555	0.1225	0.1236	-0.015	-0.0461	0.1617	-0.0351	0.1549	36.5945	1.8714	-8.1088
11	2.7061	0.6842	-0.4869	2.7882	0.2278	1.9344	-0.0041	-0.0856	-0.1199	-0.0187	-0.0146	-0.0438	0.1225	-0.0442	0.0089	0.1155	0.0061	-0.0114	0.1274	0.009	0.0793	25.955	-10.1676	-16.3237
12	2.3259	1.7899	0.9283	2.6477	2.698	4.334	-0.072	0.1683	-0.1135	0.0361	0.3007	-0.3378	-0.069	0.479	-0.1712	0.1027	0.0426	-0.0205	0.1787	0.0011	0.1803	40.7152	-8.6529	-18.7313
13	1.4619	0.0328	-1.6967	1.2673	0.4281	6.4015	-0.0414	-0.0253	-0.053	0.0459	0.0559	-0.1945	0.1274	0.149	-0.015	0.1024	0.0466	-0.022	0.1305	0.0028	0.1668	38.9249	-13.6264	-19.0498
14	2.6072	2.5989	-1.0962	3.5087	-1.3109	3.2585	0.0218	-0.0022	0.012	-0.0583	0.0076	-0.0773	0.0351	0.0996	0.0067	0.0944	0.0357	-0.0163	0.1379	0.0057	0.1305	31.8809	-8.2991	-28.1751
15	1.5857	-1.1952	-0.4208	7.7885	-0.9495	2.0984	-0.0204	-0.0034	-0.1418	-0.0717	0.0361	0.0991	0.0911	-0.0025	-0.0051	0.0747	-0.0012	-0.033	0.1302	-0.0003	0.0852	27.357	-7.4866	-30.3787
16	0.4875	0.2263	-0.0148	0.8517	0.3046	1.8991	-0.0108	0.0284	-0.0233	-0.0142	-0.0027	-0.0333	-0.058	0.0169	-0.0076	0.1404	0.008	-0.0176	0.1504	0.0019	0.1368	24.6558	1.4273	-33.1016

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 59 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 60 through 82 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 83 through 95 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 96 through 129 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 130 through 172 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 173 through 222 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 21 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 22 through 38 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 39 through 82 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 83 through 95 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 96 through 129 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 130 through 148 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 149 through 172 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 173 through 222 )

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