PDB-5fav: E491Q mutant of choline TMA-lyase

ID or keywords:

Entry

Database: PDB / ID: 5fav

Title

E491Q mutant of choline TMA-lyase

Components

Choline trimethylamine-lyase

Keywords

LYASE /

mutant / radical

Function / homology

Function and homology information

choline trimethylamine-lyase / carbon-nitrogen lyase activity / choline catabolic process /

choline binding / protein homodimerization activity
Similarity search - Function

Biological species

Desulfovibrio alaskensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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 ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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	5fav.cif.gz	956.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5fav.ent.gz	799.1 KB	Display	PDB format
PDBx/mmJSON format	5fav.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/fa/5fav ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fav	HTTPS FTP

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Related structure data

Related structure data	5fauSC 5fawC 5fayC 5kdpC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5kdp-d 6vue-d 5faw-d 5fay-d 5a0u-4 5a0u-1 21601 5ymr-1 4gz8-d 6a0r-1 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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	228.922, 228.922, 78.924
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	94
Space group name H-M	P4₂2₁2

Symmetry

Point symmetry: (Schoenflies symbol: C₂ (2 fold cyclic

))

Components on special symmetry positions

ID	Model	Components
1	1	A-1166- HOH
2	1	A-1697- HOH
3	1	A-2089- HOH
4	1	A-2228- HOH
5	1	B-1906- HOH
6	1	B-1972- HOH
7	1	B-1977- HOH

Details

Size exclusion chromatography

#1: Protein	Choline trimethylamine-lyase Mass: 91585.141 Da / Num. of mol.: 2 / Mutation: E491Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio alaskensis (bacteria) / Strain: G20 / Gene: Dde_3282 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q30W70, choline trimethylamine-lyase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-MLI / MALONATE ION / Malonic acid Mass: 102.046 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₂O₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 2367 / 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: 2.82 Å³/Da / Density % sol: 56.42 % / Description: Crystals were rod-like and grew within 7 days.
Crystal grow	Temperature: 294 K / Method: vapor diffusion Details: Protein at 8 mg/mL in buffer containing 50 mM potassium phosphate pH 8.0, 50 mM potassium chloride, and 10 mM choline was mixed in a 1:1 ratio with well solution containing 1.0-1.2 M sodium malonate pH 7.0-8.0.

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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 22, 2014
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: 1.6→50 Å / Num. obs: 272954 / % possible obs: 100 % / Redundancy: 13.1 % / R_sym value: 0.128 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.6→1.63 Å / Redundancy: 12.2 % / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau

Resolution: 1.6→49.471 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1777	8200	3 %
R_work	0.1508	-	-
obs	0.1516	272954	99.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→49.471 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12678	0	66	2367	15111

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	13140
X-RAY DIFFRACTION	f_angle_d	1.121	17801
X-RAY DIFFRACTION	f_dihedral_angle_d	13.571	4888
X-RAY DIFFRACTION	f_chiral_restr	0.042	1902
X-RAY DIFFRACTION	f_plane_restr	0.006	2334

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 (%)
1.6001-1.6183	0.2555	410	0.2543	8553	X-RAY DIFFRACTION	100
1.6183-1.6373	10000000	0	0.2423	9008	X-RAY DIFFRACTION	100
1.6373-1.6573	0.2533	410	0.2363	8601	X-RAY DIFFRACTION	100
1.6573-1.6783	0.2352	410	0.2334	8596	X-RAY DIFFRACTION	100
1.6783-1.7003	10000000	0	0.2305	9002	X-RAY DIFFRACTION	100
1.7003-1.7236	0.2463	410	0.2235	8614	X-RAY DIFFRACTION	100
1.7236-1.7483	0.2453	410	0.2154	8629	X-RAY DIFFRACTION	100
1.7483-1.7744	10000000	0	0.2102	9011	X-RAY DIFFRACTION	100
1.7744-1.8021	0.2327	410	0.2002	8629	X-RAY DIFFRACTION	100
1.8021-1.8316	0.2246	410	0.1945	8625	X-RAY DIFFRACTION	100
1.8316-1.8632	10000000	0	0.1902	9029	X-RAY DIFFRACTION	100
1.8632-1.8971	0.208	410	0.1791	8581	X-RAY DIFFRACTION	100
1.8971-1.9336	0.1916	410	0.1722	8665	X-RAY DIFFRACTION	100
1.9336-1.9731	10000000	0	0.1661	9055	X-RAY DIFFRACTION	100
1.9731-2.016	0.1746	410	0.1644	8635	X-RAY DIFFRACTION	100
2.016-2.0628	0.178	410	0.1604	8649	X-RAY DIFFRACTION	100
2.0628-2.1144	10000000	0	0.1603	9028	X-RAY DIFFRACTION	100
2.1144-2.1716	0.1851	410	0.1556	8670	X-RAY DIFFRACTION	100
2.1716-2.2355	0.1801	410	0.1522	8674	X-RAY DIFFRACTION	100
2.2355-2.3077	10000000	0	0.147	9093	X-RAY DIFFRACTION	100
2.3077-2.3901	0.1724	410	0.1384	8702	X-RAY DIFFRACTION	100
2.3901-2.4858	0.1605	410	0.1419	8691	X-RAY DIFFRACTION	100
2.4858-2.599	10000000	0	0.1458	9111	X-RAY DIFFRACTION	100
2.599-2.736	0.1768	410	0.15	8725	X-RAY DIFFRACTION	100
2.736-2.9074	0.1849	410	0.1532	8740	X-RAY DIFFRACTION	100
2.9074-3.1318	10000000	0	0.1442	9173	X-RAY DIFFRACTION	100
3.1318-3.4469	0.1662	410	0.1326	8799	X-RAY DIFFRACTION	100
3.4469-3.9455	0.1335	410	0.1152	8852	X-RAY DIFFRACTION	100
3.9455-4.9702	10000000	0	0.1047	9347	X-RAY DIFFRACTION	100
4.9702-49.4943	0.1572	410	0.1352	9267	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	0.557	-0.2759	0.2236	0.697	-0.5311	1.009	-0.0599	-0.1112	-0.0346	0.1052	0.0281	0.0006	0.1229	-0.1668	0.0218	0.2801	-0.0737	0.0257	0.1605	-0.0084	0.1728	-56.1888	-74.1056	28.1611
2	0.2462	-0.0608	-0.0849	0.2461	-0.0421	0.5721	0.0017	0.0258	-0.0827	-0.0336	-0.0097	0.0547	0.3101	-0.2354	-0.0023	0.2765	-0.0919	0.0111	0.1706	-0.0069	0.1862	-55.4212	-76.4544	11.0915
3	0.1963	-0.452	0.4052	1.8205	-1.987	3.5344	-0.0571	-0.0379	-0.0039	0.0809	0.079	0.1039	0.0427	-0.2897	-0.0383	0.1261	-0.0258	0.0139	0.167	-0.0251	0.1545	-59.1037	-55.4528	24.1504
4	0.4549	0.0056	-0.0305	0.3983	-0.0872	0.6537	0.006	-0.0529	-0.0562	0.0642	-0.0186	-0.0144	0.208	-0.0266	0.014	0.2219	-0.0204	0.009	0.1048	0.0068	0.1612	-39.1872	-71.654	28.8288
5	0.7424	-0.4748	-0.2633	0.9347	0.286	0.9172	0.0363	0.1273	-0.045	-0.1253	-0.055	-0.0954	0.2291	0.0373	0.0124	0.217	0.0011	0.0258	0.117	0.0066	0.157	-35.53	-73.2467	-2.0593
6	0.736	-0.4886	0.0749	1.0176	-0.0612	0.4518	0.0459	0.1669	-0.1283	-0.1344	-0.0821	-0.1114	0.3516	0.0848	0.0247	0.3704	0.0598	0.0502	0.1903	-0.0157	0.2311	-25.2912	-83.0642	-2.3341
7	0.4493	0.0856	-0.0873	0.4462	-0.0925	0.4807	0.0204	-0.0303	-0.1216	0.0516	-0.048	-0.0779	0.3529	0.0487	0.024	0.4158	0.0319	0.0275	0.1342	0.0149	0.252	-28.0243	-88.3049	16.5202
8	0.5846	-0.4547	-0.0357	0.4224	0.1453	0.4029	-0.0135	-0.0054	-0.0123	-0.0017	0.0112	-0.0689	0.0038	0.2414	-0.0091	0.1199	-0.0085	0.0173	0.2773	-0.0004	0.1979	3.9392	-38.1666	-4.9116
9	0.4172	-0.2788	-0.2491	0.3276	0.1716	0.8479	0.017	-0.0194	0.0986	-0.011	0.0206	-0.1391	-0.1598	0.2714	-0.0461	0.1419	-0.0465	0.0068	0.2191	-0.009	0.1934	-2.6773	-25.6427	7.2852
10	0.5138	-0.4667	-0.1848	0.5765	0.1043	0.6303	0.0751	0.08	-0.012	-0.0848	-0.0439	-0.0045	0.0016	0.1459	-0.0417	0.1178	0.0053	0.0087	0.1529	-0.0015	0.1423	-11.4372	-39.7781	-11.6249
11	0.3837	0.0021	-0.0772	0.28	-0.0509	0.5785	-0.0113	0.0017	-0.0459	-0.0014	0.0145	-0.0731	0.1215	0.2364	0.0033	0.1339	0.0538	0.0062	0.2177	-0.0065	0.1655	-1.2139	-52.9641	3.2912
12	0.2455	-0.0283	0.2367	0.1193	-0.0889	1.5504	-0.0091	-0.0445	0.006	0.0395	0.0115	0.0217	-0.0365	-0.0047	-0.002	0.1254	0.0134	0.0036	0.1438	-0.0013	0.1613	-18.4603	-36.7404	23.4844
13	0.2943	-0.1857	0.182	0.2291	-0.1076	1.2373	0.0005	-0.0334	-0.002	0.0426	0.0314	-0.0071	-0.0286	0.1862	-0.0355	0.1581	0.0116	0.0084	0.1889	0.0005	0.1788	-13.1097	-42.2055	35.4714
14	0.5022	-0.1271	-0.1129	0.8446	0.0657	0.6401	-0.0009	-0.0639	-0.0774	0.0763	0.0266	-0.1604	0.1684	0.2819	-0.0252	0.1504	0.0591	-0.0149	0.2345	0.0064	0.1703	-3.2206	-53.8569	29.0411
15	0.9683	0.4301	-0.269	1.2038	-0.147	0.9684	0.0426	-0.0599	0.013	0.0427	-0.0246	-0.2164	-0.0333	0.4288	-0.0144	0.1582	0.0351	-0.0002	0.3948	-0.0118	0.2274	8.8089	-46.3754	23.4675

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 41 through 110 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 111 through 229 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 230 through 285 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 286 through 505 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 506 through 626 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 627 through 709 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 710 through 846 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 44 through 110 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 111 through 207 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 208 through 285 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 286 through 505 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 506 through 626 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 627 through 709 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 710 through 787 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 788 through 846 )

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