PDB-5tl4: Crystal structure of Sphingomonas paucimobilis aryl O-demethylase LigM

ID or keywords:

Entry

Database: PDB / ID: 5tl4

Title

Crystal structure of Sphingomonas paucimobilis aryl O-demethylase LigM

Components

Vanillate/3-O-methylgallate O-demethylase

Keywords

TRANSFERASE /

demethylase / tetrahydrofolate-dependent / aryl

Function / homology

Function and homology information

vanillate/3-O-methylgallate O-demethylase / lignin catabolic process /

methyltransferase activity /

Biological species

Sphingomonas paucimobilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.751 Å

Authors

Kohler, A.C. / Adams, P.D. / Simmons, B.A. / Sale, K.L.

Funding support

United States, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structure of aryl O-demethylase offers molecular insight into a catalytic tyrosine-dependent mechanism.
Authors: Kohler, A.C. / Mills, M.J.L. / Adams, P.D. / Simmons, B.A. / Sale, K.L.

History

Deposition	Oct 10, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 19, 2017	Group: Database references
Revision 1.2	May 3, 2017	Group: Database references
Revision 1.3	Sep 27, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Mar 6, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tl4.cif.gz	770.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5tl4.ent.gz	633 KB	Display	PDB format
PDBx/mmJSON format	5tl4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tl/5tl4 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/5tl4	HTTPS FTP

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Related structure data

Similar structure data	6go5-2 4k4g-2 2pfn-d 4qzg-d 4qza-d 5d49-d 2pfp-d 2ve3-1 2bcr-d 5d46-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: Vanillate/3-O-methylgallate O-demethylase

B: Vanillate/3-O-methylgallate O-demethylase

C: Vanillate/3-O-methylgallate O-demethylase

D: Vanillate/3-O-methylgallate O-demethylase

hetero molecules

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

1

A: Vanillate/3-O-methylgallate O-demethylase

hetero molecules

defined by author
52.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Vanillate/3-O-methylgallate O-demethylase

hetero molecules

defined by author
52.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Vanillate/3-O-methylgallate O-demethylase

hetero molecules

defined by author
53 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Vanillate/3-O-methylgallate O-demethylase

hetero molecules

defined by author
53 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	112.837, 126.184, 155.646
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, 4 molecules ABCD

#1: Protein	Vanillate/3-O-methylgallate O-demethylase Mass: 52779.348 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas paucimobilis (bacteria) / Gene: ligM / Plasmid: pCDF-Duet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60FX1, UniProt: G2IQS7*PLUS

#1: Protein

Vanillate/3-O-methylgallate O-demethylase

Mass: 52779.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Sphingomonas paucimobilis (bacteria) / Gene: ligM / Plasmid: pCDF-Duet-1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60FX1, UniProt: G2IQS7*PLUS

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Non-polymers , 5 types, 2668 molecules

#2: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-NH4 / AMMONIUM ION / Ammonium Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H₄N
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2654 / 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: 2.62 Å³/Da / Density % sol: 53.13 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium tartrate dibasic, 20% PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.75→49.01 Å / Num. obs: 222501 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / CC_1/2: 0.99 / R_merge(I) obs: 0.175 / Net I/σ(I): 14.33
Reflection shell	Resolution: 1.75→1.81 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.23 / CC_1/2: 0.67 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.11rc2_2531: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.751→49.009 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.32
Details: TLS parameters were added in the final stages of refinement.

	R_factor	Num. reflection	% reflection
R_free	0.2122	1996	0.9 %
R_work	0.1697	-	-
obs	0.1701	222189	99.78 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.751→49.009 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14289	0	34	2654	16977

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14851
X-RAY DIFFRACTION	f_angle_d	0.782	20247
X-RAY DIFFRACTION	f_dihedral_angle_d	9.23	8724
X-RAY DIFFRACTION	f_chiral_restr	0.053	2134
X-RAY DIFFRACTION	f_plane_restr	0.006	2628

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 (%)
1.7509-1.7947	0.3503	139	0.301	15350	X-RAY DIFFRACTION	98
1.7947-1.8433	0.3141	142	0.2605	15589	X-RAY DIFFRACTION	100
1.8433-1.8975	0.2683	141	0.2325	15595	X-RAY DIFFRACTION	100
1.8975-1.9587	0.255	142	0.2104	15644	X-RAY DIFFRACTION	100
1.9587-2.0288	0.2622	143	0.1956	15648	X-RAY DIFFRACTION	100
2.0288-2.11	0.2464	142	0.1931	15726	X-RAY DIFFRACTION	100
2.11-2.206	0.231	142	0.1737	15642	X-RAY DIFFRACTION	100
2.206-2.3223	0.2334	140	0.1717	15684	X-RAY DIFFRACTION	100
2.3223-2.4678	0.2221	143	0.1673	15714	X-RAY DIFFRACTION	100
2.4678-2.6583	0.2488	143	0.1708	15729	X-RAY DIFFRACTION	100
2.6583-2.9258	0.2146	144	0.1678	15778	X-RAY DIFFRACTION	100
2.9258-3.3491	0.1916	143	0.1551	15854	X-RAY DIFFRACTION	100
3.3491-4.2192	0.1655	144	0.1348	15966	X-RAY DIFFRACTION	100
4.2192-49.0286	0.1511	148	0.1373	16274	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	0.6512	-0.2608	-0.1853	0.673	0.3438	0.4494	0.0302	-0.0374	0.0552	-0.0182	0.0114	-0.0783	-0.042	0.099	-0.0475	0.1079	-0.013	-0.0081	0.1127	0.0051	0.094	21.9458	28.5606	51.7042
2	2.7342	-3.3632	-0.718	4.3121	1.8356	7.3042	0.195	0.1594	0.116	-0.2341	-0.1484	-0.0561	-0.2629	-0.0673	-0.0417	0.1809	-0.0462	0.0442	0.1445	0.0239	0.1344	22.1925	46.6417	43.2458
3	4.1977	-3.0471	0.9143	3.2483	-1.1712	3.795	-0.0566	-0.2679	0.3361	0.1537	0.1371	-0.1246	-0.3376	0.1217	-0.0707	0.1833	-0.0898	0.0321	0.1031	-0.0104	0.1577	19.2784	47.596	55.9484
4	0.7707	-0.2987	-0.2524	0.403	0.2003	0.274	0.011	0.0546	-0.0406	-0.0419	-0.0113	0.0002	0.0041	0.0016	0.0011	0.1377	0.0007	-0.0085	0.1012	-0.0005	0.1175	13.2532	18.187	46.9184
5	0.8491	-0.254	-0.3796	1.2496	-0.0666	2.2727	-0.0316	0.0806	-0.1466	-0.0342	-0.016	0.1745	0.2022	-0.186	0.0407	0.0987	-0.0134	-0.0074	0.0896	-0.0168	0.1651	-2.0927	18.1386	49.5971
6	0.8888	-0.2596	-0.4	0.4893	0.5284	1.2345	-0.0412	-0.3053	0.0596	0.1375	0.0876	-0.0544	0.0611	0.2891	-0.0438	0.1367	0.0051	0.0011	0.2481	-0.0078	0.1311	5.7789	39.2447	87.3289
7	3.3631	-0.4323	-1.6142	2.5991	1.7621	1.7351	-0.119	-0.5329	-0.3194	0.3613	-0.0994	0.0528	0.5233	0.3057	0.1797	0.3997	0.169	0.0133	0.5187	0.1131	0.1826	9.7718	22.6056	97.129
8	2.7776	1.879	-0.3103	4.2849	0.5761	2.1686	-0.1723	-0.263	-0.2954	0.054	0.217	-0.2876	0.3784	0.4472	-0.0535	0.2697	0.1658	-0.0159	0.3692	0.0587	0.16	15.7038	21.9819	85.7019
9	0.5246	-0.0808	-0.3166	0.5729	0.5108	1.2915	0.0052	-0.0997	0.0338	0.035	-0.0278	0.0332	-0.0402	-0.0117	0.0276	0.0969	0.0061	0.0054	0.1075	-0.0039	0.1129	-9.1397	40.2315	79.7323
10	3.8793	1.9057	-2.4973	1.651	-2.0603	4.5157	0.0273	0.0278	0.0809	0.004	0.0422	0.1768	0.0481	-0.2284	-0.078	0.105	0.0235	0.005	0.0764	-0.0404	0.1329	-16.1414	37.1974	72.5144
11	0.6585	-0.3131	-0.4094	0.7071	0.2857	0.615	0.0281	0.0507	0.0266	-0.0423	0.0025	-0.0624	-0.0331	0.0214	-0.0341	0.1033	-0.0043	-0.0099	0.1233	0.0029	0.1069	21.8469	25.4828	129.1617
12	0.8117	-0.4193	-0.4082	1.1484	0.2007	0.8794	0.0589	0.0442	0.1826	-0.0838	0.028	-0.1153	-0.1405	0.0516	-0.0855	0.1096	-0.0237	0.0144	0.1153	-0.0031	0.1355	28.4336	32.5733	130.0463
13	2.0925	-1.7745	-0.0005	6.2343	2.5363	3.6986	0.1855	0.2968	0.266	-0.4981	-0.1317	-0.0924	-0.4091	-0.0303	-0.0466	0.2409	-0.0054	0.0813	0.1776	0.0659	0.2037	24.8653	46.1392	121.0642
14	3.5616	-2.9466	1.6616	4.5233	-2.1356	5.0323	-0.0955	-0.1565	0.4208	0.1466	0.1721	-0.113	-0.3855	-0.0597	-0.0716	0.1731	-0.052	0.0665	0.0823	0.0108	0.2326	21.9645	47.5137	133.8396
15	0.8639	-0.2843	-0.3523	0.4204	0.1553	0.5109	0.0126	0.1946	-0.0796	-0.0736	-0.0387	-0.0035	0.0164	-0.0762	0.0276	0.1211	-0.0096	0.0098	0.1296	-0.0181	0.1162	15.7165	18.1732	124.7509
16	1.3158	-0.4669	-0.2514	1.7859	0.3309	1.7494	-0.0071	0.2199	-0.177	-0.0592	-0.0562	0.1352	0.1232	-0.1921	0.0547	0.0828	-0.0199	0.0035	0.1376	-0.0314	0.1286	1.8047	18.1928	129.5565
17	1.2793	0.5825	-0.2777	2.6639	-0.3593	1.5517	-0.0645	0.4489	-0.1391	-0.4378	0.1068	0.3614	0.2011	-0.5004	-0.0607	0.1505	-0.0029	-0.0073	0.3376	-0.0624	0.2275	-3.039	18.5033	122.2917
18	0.5827	-0.2201	-0.1661	0.6115	0.4961	0.9601	-0.0011	-0.0598	0.0989	0.0205	0.0215	-0.0113	-0.0416	0.07	-0.0173	0.0909	-0.0099	0.0082	0.1175	-0.0008	0.1294	4.9829	40.6214	163.3554
19	0.8514	-0.3706	-0.2591	1.2259	0.2319	1.4499	-0.0263	-0.1173	0.0295	0.1233	0.0449	-0.1	0.0449	0.1931	-0.0198	0.0952	0.0162	-0.009	0.1498	-0.0113	0.1111	12.9636	37.4441	167.7467
20	5.4812	-0.4503	-4.6117	4.7358	1.7784	4.3559	-0.0886	-0.0874	-0.2052	0.1197	-0.0278	0.0995	0.4385	0.1579	0.0989	0.2271	0.055	-0.0189	0.2103	0.0474	0.0885	12.0946	22.4511	174.8335
21	3.8539	3.4603	-0.2249	5.7534	1.1443	2.3257	-0.0795	0.0963	-0.2725	-0.0274	0.219	-0.4021	0.3438	0.3112	-0.1366	0.1903	0.1	-0.026	0.1759	0.0375	0.1188	18.0394	21.9567	163.5991
22	0.4685	-0.0469	-0.1423	0.443	0.3105	0.743	0.0045	0.0056	0.0484	-0.005	-0.0418	0.0636	-0.0463	-0.1074	0.0444	0.1226	0.0156	0.0048	0.129	-0.0043	0.1399	-8.1069	39.7368	156.0164

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 179 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 180 through 212 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 213 through 237 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 238 through 354 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 355 through 467 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 3 through 179 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 180 through 212 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 213 through 237 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 238 through 409 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 410 through 454 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 106 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 107 through 179 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 180 through 212 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 213 through 237 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 238 through 354 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 355 through 433 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 434 through 467 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 3 through 106 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 107 through 179 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 180 through 212 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 213 through 237 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 238 through 454 )

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