PDB-5fau: wild-type choline TMA lyase in complex with choline

ID or keywords:

Entry

Database: PDB / ID: 5fau

Title

wild-type choline TMA lyase in complex with choline

Components

Choline trimethylamine-lyase

Keywords

LYASE / radical / barrel

Function / homology

Function and homology information

choline trimethylamine-lyase / choline trimethylamine lyase activity / carbon-nitrogen lyase activity / choline catabolic process / choline binding / protein homodimerization activity / cytosol
Similarity search - Function

Biological species

Desulfovibrio alaskensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Funk, M.A. / Drennan, C.L.

Funding support

United States, 1items

Citation

Journal: Cell Chem Biol / Year: 2016
Title: Molecular Basis of C-N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase.
Authors: Bodea, S. / Funk, M.A. / Balskus, E.P. / Drennan, C.L.

History

Deposition	Dec 12, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 2, 2016	Group: Database references
Revision 1.2	Sep 20, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Nov 1, 2017	Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Sep 27, 2023	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	5fau.cif.gz	1.8 MB	Display	PDBx/mmCIF format
PDB format	pdb5fau.ent.gz	1.5 MB	Display	PDB format
PDBx/mmJSON format	5fau.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5fau_validation.pdf.gz	488.7 KB	Display	wwPDB validaton report
Full document	5fau_full_validation.pdf.gz	502.8 KB	Display
Data in XML	5fau_validation.xml.gz	128.3 KB	Display
Data in CIF	5fau_validation.cif.gz	190.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fa/5fau ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fau	HTTPS FTP

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Related structure data

Related structure data	5favC 5fawC 5fayC 5kdpC 1r8wS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6nd3-2 5a0u-2 6nd3-3 5a0u-3 6nd3-1 6xs4-d 1r9d-d 4mtj-d 6nd3-4 5a0u-5 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: Choline trimethylamine-lyase

B: Choline trimethylamine-lyase

C: Choline trimethylamine-lyase

D: Choline trimethylamine-lyase

hetero molecules

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

1

A: Choline trimethylamine-lyase

C: Choline trimethylamine-lyase

hetero molecules

defined by author&software
Evidence: gel filtration
191 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Choline trimethylamine-lyase

D: Choline trimethylamine-lyase

hetero molecules

defined by author&software
Evidence: gel filtration
191 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.607, 234.871, 104.994
Angle α, β, γ (deg.)	90.00, 109.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

by size exclusion chromatography

#1: Protein	Choline trimethylamine-lyase Mass: 95002.961 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio alaskensis (strain G20) (bacteria) Strain: G20 / Gene: Dde_3282 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q30W70, choline trimethylamine-lyase
#2: Chemical	ChemComp-CHT / CHOLINE ION Mass: 104.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₁₄NO
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2486 / 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: 2.43 Å³/Da / Density % sol: 49.45 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion / pH: 8 Details: 20% (v/v) glycerol, 25% (w/v) PEG 8000, 0.5 M lithium chloride, 0.1 M Tris pH 8.0; 10 mM choline was included in cryoprotectant

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2013
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. obs: 282449 / % possible obs: 99.3 % / Redundancy: 6.7 % / R_sym value: 0.09 / Net I/σ(I): 12.5
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 5.9 % / R_merge(I) obs: 0.986 / Mean I/σ(I) obs: 1.55 / % possible all: 99.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1R8W

1r8w

Resolution: 1.9→50 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / Phase error: 17.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1689	8478	3 %
R_work	0.1449	-	-
obs	0.1456	282449	99.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.9→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25070	0	76	2486	27632

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	25755
X-RAY DIFFRACTION	f_angle_d	0.925	34877
X-RAY DIFFRACTION	f_dihedral_angle_d	14.771	15495
X-RAY DIFFRACTION	f_chiral_restr	0.155	3743
X-RAY DIFFRACTION	f_plane_restr	0.006	4531

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 (%)
1.8987-1.9203	0.3371	274	0.2773	8860	X-RAY DIFFRACTION	97
1.9203-1.9429	0.3294	266	0.2682	9252	X-RAY DIFFRACTION	99
1.9429-1.9666	0.2664	306	0.2413	9006	X-RAY DIFFRACTION	99
1.9666-1.9915	0.2557	280	0.2223	9158	X-RAY DIFFRACTION	100
1.9915-2.0177	0.2371	269	0.2097	9119	X-RAY DIFFRACTION	99
2.0177-2.0454	0.223	290	0.2063	9106	X-RAY DIFFRACTION	99
2.0454-2.0746	0.2297	284	0.2	9024	X-RAY DIFFRACTION	99
2.0746-2.1055	0.201	264	0.1847	9178	X-RAY DIFFRACTION	100
2.1055-2.1384	0.2148	288	0.1715	9170	X-RAY DIFFRACTION	100
2.1384-2.1735	0.1778	294	0.1637	9139	X-RAY DIFFRACTION	100
2.1735-2.211	0.1919	270	0.16	9186	X-RAY DIFFRACTION	100
2.211-2.2512	0.2185	281	0.1715	9117	X-RAY DIFFRACTION	100
2.2512-2.2945	0.1763	302	0.1527	9162	X-RAY DIFFRACTION	100
2.2945-2.3413	0.1717	275	0.1461	9209	X-RAY DIFFRACTION	100
2.3413-2.3922	0.1706	284	0.1402	9053	X-RAY DIFFRACTION	99
2.3922-2.4479	0.186	273	0.144	9170	X-RAY DIFFRACTION	99
2.4479-2.5091	0.1764	274	0.141	9050	X-RAY DIFFRACTION	98
2.5091-2.5769	0.1767	292	0.1397	9151	X-RAY DIFFRACTION	100
2.5769-2.6527	0.1688	282	0.1388	9189	X-RAY DIFFRACTION	100
2.6527-2.7384	0.1589	283	0.1405	9143	X-RAY DIFFRACTION	100
2.7384-2.8362	0.1924	293	0.1405	9190	X-RAY DIFFRACTION	100
2.8362-2.9498	0.1706	283	0.1373	9146	X-RAY DIFFRACTION	99
2.9498-3.084	0.1618	281	0.1361	9159	X-RAY DIFFRACTION	100
3.084-3.2466	0.1627	278	0.1348	8989	X-RAY DIFFRACTION	98
3.2466-3.4499	0.1693	280	0.1383	9227	X-RAY DIFFRACTION	100
3.4499-3.7162	0.1402	280	0.1275	9167	X-RAY DIFFRACTION	100
3.7162-4.09	0.1439	296	0.1179	9150	X-RAY DIFFRACTION	100
4.09-4.6815	0.1253	287	0.1127	9186	X-RAY DIFFRACTION	99
4.6815-5.8967	0.1477	288	0.1296	9109	X-RAY DIFFRACTION	99
5.8967-49.6637	0.1517	281	0.1524	9206	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	1.146	0.772	0.5192	0.7685	0.6421	0.5706	-0.068	0.2874	-0.0072	-0.3824	0.1816	0.2964	0.1694	-0.2201	0.0431	0.5348	-0.1917	-0.1939	0.4803	0.0582	0.3269	-52.8049	-3.399	49.3283
2	0.8532	0.1557	0.042	0.686	0.0153	0.5366	-0.0726	0.3447	-0.0031	-0.526	0.1937	0.0638	0.1125	-0.1042	-0.0839	0.5535	-0.144	-0.0687	0.4145	0.0133	0.2322	-38.4147	0.8766	48.0768
3	1.128	0.738	0.1797	1.0258	0.3936	0.7123	-0.0223	0.1157	0.1784	-0.2161	0.1028	0.3468	0.007	-0.2055	-0.0085	0.2762	-0.0582	-0.0785	0.2954	0.0928	0.2933	-50.4958	7.8063	66.1465
4	0.718	0.1662	0.0729	0.9595	-0.0888	0.515	-0.0353	0.1656	-0.0803	-0.3175	0.1926	0.2875	0.2322	-0.2826	-0.1554	0.3963	-0.1502	-0.1444	0.3879	0.0482	0.3468	-53.8574	-14.0167	64.403
5	0.8462	0.0284	-0.2624	1.5594	0.0382	0.8219	-0.0895	0.1489	-0.3246	-0.4075	0.0929	-0.3471	0.3481	0.0973	-0.0097	0.4829	-0.0403	0.0483	0.2815	-0.1107	0.3757	-21.9526	-20.2826	61.4443
6	1.0606	0.1093	0.1929	0.4703	0.3046	0.6917	-0.0515	0.3189	-0.3127	-0.4739	0.17	0.0129	0.4223	-0.1869	-0.1315	0.7538	-0.176	-0.092	0.3994	-0.0889	0.4405	-41.1223	-31.3455	56.4431
7	0.4717	0.0528	-0.0572	2.4511	0.2997	0.3554	0.0991	-0.1584	0.0511	0.552	-0.0451	0.1491	-0.1972	0.0833	-0.0595	0.4282	-0.0604	0.0749	0.2734	0.0024	0.1737	-28.3651	27.1035	126.4859
8	0.7845	-0.1447	-0.2719	1.3348	0.0608	0.655	0.1003	-0.2464	-0.083	0.4747	-0.0598	-0.0342	-0.1521	0.1342	-0.052	0.3791	-0.0811	-0.0421	0.3073	0.0313	0.1853	-16.008	17.9393	126.6505
9	0.7047	-0.2824	-0.2279	2.0454	0.2928	0.5758	0.097	-0.0811	0.0118	0.22	-0.046	0.4376	-0.0895	-0.099	0.0278	0.2169	-0.0141	0.0594	0.2096	0.0409	0.2291	-36.6114	22.5288	112.5275
10	1.2028	0.1421	-0.2281	0.0589	0.2326	1.7354	0.1329	-0.1646	0.1299	0.3801	-0.0531	0.387	-0.3721	-0.0702	-0.0524	0.4713	-0.0375	0.1654	0.2631	-0.0013	0.3082	-37.7244	39.0566	123.1199
11	0.6702	0.052	-0.0635	1.3013	-0.0977	0.5053	0.0692	-0.0845	0.1009	0.2204	0.0112	0.0241	-0.2469	0.0354	-0.0852	0.3532	-0.0561	0.054	0.251	-0.0182	0.2019	-20.3441	41.4133	110.8813
12	1.4695	0.5437	-0.0754	1.0627	-0.181	0.6037	0.0492	-0.055	-0.127	0.1018	-0.087	-0.4266	-0.1132	0.2874	0.015	0.2002	-0.0682	-0.0354	0.2966	0.0113	0.2957	2.4815	23.6605	105.7056
13	0.9552	-0.0965	0.0027	0.9859	-0.0893	0.8406	0.0849	-0.2352	0.1112	0.3575	-0.0685	-0.2644	-0.2771	0.1488	-0.0168	0.4571	-0.169	-0.0298	0.37	-0.0361	0.2917	-0.3038	43.1122	115.3277
14	0.6532	0.1842	0.0252	0.7538	0.1233	0.5369	-0.1221	0.2453	-0.0362	-0.415	0.1689	-0.0453	-0.0816	0.0829	-0.0475	0.4324	-0.0985	0.0358	0.319	-0.0262	0.1725	-16.369	30.3281	51.7682
15	1.0399	0.7687	-0.0737	0.7762	-0.1048	0.2453	-0.0798	0.1953	-0.2929	-0.2828	0.152	-0.3562	0.0548	0.1206	0.0272	0.2932	-0.017	0.0779	0.2842	-0.1095	0.2796	-5.7137	16.6217	63.973
16	0.4287	0.3235	-0.0168	0.6807	0.1787	0.582	-0.0945	0.2196	-0.1196	-0.2644	0.158	-0.2447	-0.0764	0.225	-0.0542	0.3103	-0.0758	0.1132	0.3321	-0.0742	0.2557	1.7166	34.5687	62.0403
17	0.6886	0.1502	-0.0293	0.7404	0.0589	0.4401	0.0052	-0.0003	0.1456	-0.0438	0.0397	0.1028	-0.1052	0.0178	-0.0444	0.2539	-0.0268	0.0338	0.2015	-0.0016	0.1914	-22.9404	45.1713	75.7092
18	1.8976	0.3072	0.0229	1.8824	-0.366	2.0433	-0.109	0.3946	0.2245	-0.4209	0.1183	0.0396	-0.2581	0.0273	-0.0405	0.4203	-0.0624	0.0607	0.2733	0.0354	0.2658	-14.4322	57.0008	62.0058
19	0.6975	-0.0151	-0.0757	2.0454	-0.0848	0.5427	-0.0033	-0.1099	-0.24	0.2093	-0.0177	-0.2774	0.0119	0.0796	0.0092	0.1547	-0.0007	-0.0521	0.2816	0.048	0.3163	-16.4614	-23.1183	115.8508
20	0.5754	0.2632	-0.2231	1.0927	-0.1033	0.3489	0.0062	-0.1132	-0.1375	0.162	-0.0318	-0.1759	-0.0111	0.1123	0.0305	0.1389	-0.0113	-0.0463	0.2447	0.0181	0.2188	-20.7163	-14.4265	113.5593
21	1.8075	-1.2416	0.4256	2.263	-0.0655	1.239	-0.003	-0.1095	-0.5021	-0.0053	-0.0429	-0.4015	0.1909	0.242	0.0654	0.1597	0.006	0.0027	0.3011	0.0662	0.552	-8.0926	-32.4959	106.7785
22	0.4544	0.2884	-0.2381	0.8375	0.1894	1.0931	-0.0891	0.0092	-0.2549	0.0001	0.0107	-0.1452	0.1139	0.093	0.0722	0.1714	0.0072	0.0112	0.2506	0.0135	0.3601	-22.3909	-31.8084	103.7602
23	0.7057	0.2329	-0.134	0.8755	-0.0658	0.4742	-0.0444	0.0759	-0.0512	-0.0448	0.0482	0.2363	0.0106	-0.1218	-0.0014	0.1263	-0.0163	-0.0303	0.2086	0.01	0.2711	-44.0853	-19.628	100.6249
24	0.9009	0.1349	-0.1641	0.8987	-0.1862	1.0196	-0.0461	0.0435	-0.157	0.0102	0.0443	0.1782	0.1175	-0.0582	-0.0022	0.1675	-0.0214	-0.0037	0.213	0.0094	0.3531	-46.5178	-35.3928	105.2067

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 53 through 95 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 96 through 207 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 208 through 285 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 286 through 505 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 506 through 719 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 720 through 846 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 52 through 110 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 111 through 207 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 208 through 284 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 285 through 330 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 331 through 505 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 506 through 708 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 709 through 846 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 52 through 207 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 208 through 284 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 285 through 400 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 401 through 787 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 788 through 846 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 52 through 110 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 111 through 284 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 285 through 330 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 331 through 401 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 402 through 709 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 710 through 846 )

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi