PDB-6htk: X-ray structure of the tryptophan lyase NosL in complex with (R)-...

ID or keywords:

Entry

Database: PDB / ID: 6htk

Title

X-ray structure of the tryptophan lyase NosL in complex with (R)-(+)-indoline-2-carboxylate

Components

3-methyl-2-indolic acid synthase

Keywords

ANTIBIOTIC /

Radical SAM / FeS cluster /

Nosiheptide

Function / homology

Function and homology information

4 iron, 4 sulfur cluster binding /

metal ion binding
Similarity search - Function

Biological species

Streptomyces actuosus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Amara, P. / Mouesca, J.M. / Bella, M. / Martin, L. / Saragaglia, C. / Gambarelli, S. / Nicolet, Y.

Funding support

France, 1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2018
Title: Radical S-Adenosyl-l-methionine Tryptophan Lyase (NosL): How the Protein Controls the Carboxyl Radical •CO2-Migration.
Authors: Amara, P. / Mouesca, J.M. / Bella, M. / Martin, L. / Saragaglia, C. / Gambarelli, S. / Nicolet, Y.

History

Deposition	Oct 4, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 21, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 28, 2018	Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.title
Revision 1.2	Apr 24, 2019	Group: Data collection / Database references / Category: citation / pdbx_database_proc Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2024	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_alt_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6htk.cif.gz	341.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6htk.ent.gz	276.5 KB	Display	PDB format
PDBx/mmJSON format	6htk.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ht/6htk ftp://data.pdbj.org/pub/pdb/validation_reports/ht/6htk	HTTPS FTP

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Related structure data

Related structure data	6htmC 6htoC 4r34S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6htm-2 6htm-1 4r33-2 4r33-1 2azq-1 4r34-1 4r34-2 6hto-d 5m8c-d 7lr6-2 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
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: 3-methyl-2-indolic acid synthase

B: 3-methyl-2-indolic acid synthase

hetero molecules

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

1

A: 3-methyl-2-indolic acid synthase

hetero molecules

A: 3-methyl-2-indolic acid synthase

hetero molecules

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

2

B: 3-methyl-2-indolic acid synthase

hetero molecules

B: 3-methyl-2-indolic acid synthase

hetero molecules

defined by author&software
93.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.650, 47.010, 114.080
Angle α, β, γ (deg.)	90.00, 108.91, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	A-756- HOH
2	1	A-940- HOH
3	1	A-943- HOH
4	1	B-795- HOH
5	1	B-986- HOH
6	1	B-1016- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	3-methyl-2-indolic acid synthase / NosL Mass: 44662.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces actuosus (bacteria) / Gene: nosL, nocL, DMT42_23170 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C6FX51

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Non-polymers , 10 types, 847 molecules

#2: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-BR / BROMIDE ION / Bromide Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#7: Chemical	ChemComp-MET / METHIONINE / Methionine Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₁NO₂S
#8: Chemical	ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₃
#9: Chemical	ChemComp-ICB / 1H-indole-2-carboxylic acid Mass: 161.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₇NO₂
#10: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#11: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 823 / 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: 53.12 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 14-20% PEG 3350, 0.2 M KBr, 1 mM S-adenosyl-L-methionine (SAM) 15 mg/mL SaNosL (protein buffer: 50 mM Tris pH 8; 150 mM NaCl and 2 mM DTT) 5 equivalents of (R)-(+)-indoline-2-carboxylic acid

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.980023 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.980023 Å / Relative weight: 1
Reflection	Resolution: 2→47.109 Å / Num. obs: 124568 / % possible obs: 99.8 % / Redundancy: 5.58 % / R_sym value: 0.098 / Net I/σ(I): 13.18
Reflection shell	Resolution: 2→2.05 Å / R_sym value: 0.695

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4R34

4r34

Resolution: 2→47.109 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 20.79

	R_factor	Num. reflection	% reflection
R_free	0.1971	6246	5.01 %
R_work	0.1689	-	-
obs	0.1704	124568	99.08 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2→47.109 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5910	0	185	823	6918

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	6355
X-RAY DIFFRACTION	f_angle_d	0.646	8645
X-RAY DIFFRACTION	f_dihedral_angle_d	17.149	3807
X-RAY DIFFRACTION	f_chiral_restr	0.043	943
X-RAY DIFFRACTION	f_plane_restr	0.003	1135

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 (%)
2.0001-2.0228	0.3374	212	0.309	3914	X-RAY DIFFRACTION	98
2.0228-2.0466	0.2839	212	0.2632	3984	X-RAY DIFFRACTION	100
2.0466-2.0716	0.2821	207	0.2592	3902	X-RAY DIFFRACTION	99
2.0716-2.0978	0.2607	205	0.2434	3905	X-RAY DIFFRACTION	100
2.0978-2.1254	0.2762	213	0.2291	4038	X-RAY DIFFRACTION	100
2.1254-2.1545	0.2613	214	0.2288	4009	X-RAY DIFFRACTION	100
2.1545-2.1853	0.2318	199	0.2211	3851	X-RAY DIFFRACTION	99
2.1853-2.2179	0.217	215	0.216	4012	X-RAY DIFFRACTION	100
2.2179-2.2526	0.2429	208	0.2071	3943	X-RAY DIFFRACTION	99
2.2526-2.2895	0.248	205	0.2031	3954	X-RAY DIFFRACTION	99
2.2895-2.329	0.2278	211	0.1988	3958	X-RAY DIFFRACTION	100
2.329-2.3713	0.2404	208	0.194	3987	X-RAY DIFFRACTION	100
2.3713-2.4169	0.2095	211	0.1859	3939	X-RAY DIFFRACTION	99
2.4169-2.4663	0.213	216	0.1823	4006	X-RAY DIFFRACTION	99
2.4663-2.5199	0.2578	209	0.1841	3947	X-RAY DIFFRACTION	100
2.5199-2.5785	0.2516	207	0.1871	3965	X-RAY DIFFRACTION	100
2.5785-2.643	0.2221	209	0.1808	3927	X-RAY DIFFRACTION	99
2.643-2.7144	0.2482	205	0.1764	3947	X-RAY DIFFRACTION	99
2.7144-2.7943	0.2356	211	0.1744	3972	X-RAY DIFFRACTION	99
2.7943-2.8845	0.2005	207	0.1729	3881	X-RAY DIFFRACTION	99
2.8845-2.9875	0.2184	208	0.1669	3986	X-RAY DIFFRACTION	99
2.9875-3.1071	0.2162	208	0.1632	3962	X-RAY DIFFRACTION	99
3.1071-3.2485	0.1759	202	0.1572	3895	X-RAY DIFFRACTION	99
3.2485-3.4197	0.1771	208	0.1435	3966	X-RAY DIFFRACTION	99
3.4197-3.6339	0.1598	209	0.1374	3953	X-RAY DIFFRACTION	99
3.6339-3.9144	0.1542	206	0.1275	3874	X-RAY DIFFRACTION	98
3.9144-4.308	0.1474	206	0.1266	3924	X-RAY DIFFRACTION	99
4.308-4.9309	0.1242	206	0.1212	3906	X-RAY DIFFRACTION	99
4.9309-6.2101	0.1479	209	0.1457	3944	X-RAY DIFFRACTION	99
6.2101-47.1218	0.1879	200	0.1683	3871	X-RAY DIFFRACTION	97

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	1.1701	-0.3827	-0.5406	0.8836	1.0553	4.1604	0.48	-0.2368	0.2118	0.229	-0.1	-0.4053	-0.5459	0.8829	-0.325	0.4803	-0.2525	0.0212	0.6601	-0.0859	0.4693	70.1333	63.2452	38.9784
2	1.0997	0.3649	-0.5828	0.5699	0.217	1.5001	0.2771	0.037	0.2553	0.0892	-0.0341	0.0402	-0.3027	-0.0376	-0.1883	0.4148	0.0421	0.0968	0.2539	0.0515	0.1981	38.4566	55.2981	41.4221
3	1.7293	0.1463	-0.893	1.0359	0.0548	1.4161	0.3694	-0.1091	0.331	0.1127	-0.0467	-0.093	-0.4686	0.2233	-0.2581	0.4594	-0.0307	0.1137	0.2759	-0.0156	0.2318	48.1771	60.5306	40.9107
4	6.1243	-2.27	-0.1291	3.3164	-0.3795	6.8	0.1001	0.3253	-0.4382	-0.124	0.1106	0.1548	0.3323	-0.1584	-0.076	0.271	0.0042	-0.0138	0.2719	-0.0032	0.1344	43.1546	43.0574	27.0889
5	6.2243	0.603	0.6691	1.1167	-0.0596	1.4773	0.0522	-0.6199	-0.4187	0.2598	0.1208	0.3943	-0.0634	-0.3997	-0.162	0.2597	0.0095	0.0604	0.4173	0.1561	0.3545	8.6699	36.8497	18.9447
6	2.3048	0.241	0.0226	0.7278	-0.2712	0.585	-0.0604	0.0507	-0.1813	-0.0408	0.0217	0.01	0.0226	-0.0193	0.0437	0.1126	-0.0061	-0.029	0.168	-0.0367	0.1425	31.9908	45.3157	-0.0478
7	2.6799	0.3637	-0.0795	2.1492	-0.0685	1.5812	-0.0847	-0.1765	-0.5071	0.2592	0.0465	0.0306	0.1732	-0.0394	0.0176	0.1004	0.03	-0.0097	0.1896	0.0366	0.2271	27.9207	35.9196	8.4004
8	2.1773	-0.0682	0.2936	1.2592	0.2186	1.6419	-0.0283	-0.1897	-0.5493	0.0292	0.0094	0.0685	0.0793	-0.0699	0.043	0.1278	-0.0021	0.0005	0.1772	0.0479	0.2609	24.5781	35.4984	8.4337
9	2.2292	0.3129	-0.0265	1.0195	-0.3485	1.1542	-0.1064	0.3322	-0.1116	-0.137	0.0872	0.1384	0.0273	-0.1538	0.0285	0.1219	-0.0156	-0.0481	0.2107	-0.0196	0.1939	18.0826	46.9926	-5.6701
10	4.3542	1.4124	-3.369	9.0864	4.9242	6.803	0.7357	-1.7782	-0.7834	0.392	-0.541	0.1278	1.2703	-1.2649	-0.208	0.6754	-0.3941	-0.149	0.7213	-0.0146	0.7591	31.5251	36.5567	0.7926
11	2	2	2	2	2.5204	2	-2.4164	3.6387	1.8303	-0.1212	1.5278	-0.0242	-2.0005	10.2894	0.8949	1.1969	-0.1746	0.3973	1.1687	0.1014	0.9281	40.5969	63.7423	43.4515
12	5.4651	-0.7667	5.9639	2.0147	-0.0834	6.8056	0.0264	0.0564	0.0216	-0.0141	0.0051	-0.0694	-0.0319	-0.0813	-0.0048	0.7182	0.0501	0.2508	0.2762	0.0489	0.3484	38.8241	67.5593	42.5848
13	6.5993	-4.783	6.735	3.6317	-4.843	6.9021	-0.0625	0.0351	-0.1088	-0.0341	0.0826	-0.0567	-0.02	-0.0761	0.0248	0.1775	-0.0037	-0.0072	0.215	-0.0615	0.3128	32.1742	32.7295	-1.0912

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 15 through 64 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 65 through 167 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 168 through 365 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 366 through 398 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 13 through 64 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 65 through 190 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 191 through 215 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 216 through 298 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 299 through 393 )
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 501 through 501 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 501 through 501 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 2460)
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 2460)

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Yorodumi