PDB-6htm: X-ray structure of the tryptophan lyase NosL in complex with boun...

ID or keywords:

Entry

Database: PDB / ID: 6htm

Title

X-ray structure of the tryptophan lyase NosL in complex with bound tryptamin

Components

3-methyl-2-indolic acid synthase

Keywords

ANTIBIOTIC /

Radical SAM / tryptophan lyase /

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: 1.7 Å

Authors

Amara, P. / Mouesca, J.M. / Bella, M. / 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_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_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.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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PDBx/mmCIF format	6htm.cif.gz	335.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6htm.ent.gz	270.4 KB	Display	PDB format
PDBx/mmJSON format	6htm.json.gz		Tree view	PDBx/mmJSON format
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Validation report

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

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Related structure data

Related structure data	6htkC 6htoC 4r34S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4r34-1 6htk-1 4r33-1 4r33-2 4r34-2 2azq-1 6hto-d 6mm8-d 6htk-2 7ajk-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) 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

92.4 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
92.1 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
92.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	94.530, 47.140, 113.900
Angle α, β, γ (deg.)	90.00, 108.90, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	A-2780- HOH
2	1	B-808- HOH
3	1	B-1008- HOH
4	1	B-1035- 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 , 9 types, 830 molecules

#2: Chemical	ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE / Tryptamine Mass: 160.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₂N₂
#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Chemical	ChemComp-MET / METHIONINE / Methionine Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₁NO₂S
#5: Chemical	ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₃
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-BR / BROMIDE ION / Bromide Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#8: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Cl
#9: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#10: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 804 / 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: 52.97 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 14-20% PEG 3350, 0.2 M KBr, 1 mM 5'- deoxyadenosine, 1 mM L-methionine, 15 mg/mL SaNosL (protein buffer: 50 mM Tris pH 8; 150 mM NaCl and 2 mM DTT), 10 mM tryptamine

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 22, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.7→47.048 Å / Num. obs: 199118 / % possible obs: 99.5 % / Redundancy: 4.01 % / R_sym value: 0.062 / Net I/σ(I): 13.09
Reflection shell	Resolution: 1.7→1.74 Å / R_sym value: 0.761

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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: 1.7→47.048 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.97 / Phase error: 20.82

	R_factor	Num. reflection	% reflection
R_free	0.1887	9730	4.89 %
R_work	0.1624	-	-
obs	0.1638	199118	97.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.7→47.048 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5925	0	142	804	6871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.019	6251
X-RAY DIFFRACTION	f_angle_d	1.468	8493
X-RAY DIFFRACTION	f_dihedral_angle_d	17.583	3748
X-RAY DIFFRACTION	f_chiral_restr	0.123	929
X-RAY DIFFRACTION	f_plane_restr	0.01	1114

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 (%)
1.7-1.7193	0.3204	271	0.3112	6059	X-RAY DIFFRACTION	94
1.7193-1.7395	0.3311	321	0.3034	6312	X-RAY DIFFRACTION	96
1.7395-1.7607	0.3588	317	0.2901	6315	X-RAY DIFFRACTION	97
1.7607-1.783	0.3064	267	0.2918	6254	X-RAY DIFFRACTION	96
1.783-1.8065	0.3164	317	0.303	6293	X-RAY DIFFRACTION	97
1.8065-1.8312	0.3015	333	0.2834	6216	X-RAY DIFFRACTION	96
1.8312-1.8574	0.27	316	0.2757	6222	X-RAY DIFFRACTION	96
1.8574-1.8851	0.3198	329	0.2521	6229	X-RAY DIFFRACTION	95
1.8851-1.9146	0.2538	319	0.2271	6015	X-RAY DIFFRACTION	95
1.9146-1.946	0.2406	306	0.2075	6324	X-RAY DIFFRACTION	97
1.946-1.9795	0.2245	337	0.1969	6355	X-RAY DIFFRACTION	98
1.9795-2.0155	0.2234	321	0.1869	6246	X-RAY DIFFRACTION	97
2.0155-2.0543	0.209	353	0.1763	6544	X-RAY DIFFRACTION	99
2.0543-2.0962	0.1854	312	0.1756	6253	X-RAY DIFFRACTION	98
2.0962-2.1418	0.2068	343	0.1732	6540	X-RAY DIFFRACTION	99
2.1418-2.1916	0.2006	329	0.1605	6268	X-RAY DIFFRACTION	98
2.1916-2.2464	0.1774	333	0.1585	6435	X-RAY DIFFRACTION	98
2.2464-2.3071	0.2153	334	0.1634	6215	X-RAY DIFFRACTION	97
2.3071-2.375	0.1876	341	0.1545	6424	X-RAY DIFFRACTION	98
2.375-2.4517	0.1907	329	0.156	6229	X-RAY DIFFRACTION	97
2.4517-2.5393	0.1923	329	0.1578	6403	X-RAY DIFFRACTION	99
2.5393-2.641	0.1769	329	0.155	6465	X-RAY DIFFRACTION	99
2.641-2.7612	0.2046	333	0.1488	6367	X-RAY DIFFRACTION	99
2.7612-2.9067	0.1748	328	0.1451	6347	X-RAY DIFFRACTION	97
2.9067-3.0888	0.1554	335	0.1394	6396	X-RAY DIFFRACTION	99
3.0888-3.3272	0.1767	333	0.143	6336	X-RAY DIFFRACTION	98
3.3272-3.6619	0.1646	340	0.1325	6422	X-RAY DIFFRACTION	99
3.6619-4.1915	0.1356	317	0.1226	6306	X-RAY DIFFRACTION	97
4.1915-5.2798	0.1426	338	0.1249	6404	X-RAY DIFFRACTION	98
5.2798-47.0656	0.1857	320	0.167	6194	X-RAY DIFFRACTION	96

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	1.6049	0.1007	-0.9644	0.7493	0.4494	3.6313	0.3428	-0.3698	0.0793	0.102	-0.045	-0.4112	-0.3977	0.8093	-0.3039	0.3736	-0.2071	-0.0034	0.613	-0.0857	0.4154	69.9851	63.3541	38.9478
2	0.9851	0.1657	-0.6397	0.6629	0.1829	1.4751	0.1507	-0.065	0.0613	0.1003	-0.0274	-0.0229	-0.2016	0.0709	-0.1115	0.281	0.0081	0.0142	0.1888	0.0112	0.1401	39.5343	54.6547	43.7573
3	1.8018	-0.0085	-0.5452	1.158	0.5905	1.5059	0.3183	-0.2308	0.3264	0.129	-0.0211	-0.1264	-0.5161	0.3648	-0.2831	0.4178	-0.1215	0.0704	0.3155	-0.0553	0.2347	51.6182	66.294	46.4763
4	1.9486	0.0323	-0.6338	1.2384	0.4627	1.4486	0.2111	0.015	0.0717	-0.071	0.0184	-0.102	-0.4527	0.1279	-0.2055	0.3148	-0.0321	0.0508	0.2264	-0.0122	0.1513	51.5365	59.6261	32.3033
5	1.7873	-0.5719	-0.3214	3.3166	1.4812	2.1397	0.2158	0.2494	0.09	-0.5202	-0.1219	0.0174	-0.3361	-0.3533	-0.101	0.3964	0.0717	0.0202	0.2966	0.049	0.1866	33.1727	56.3936	29.0838
6	5.4572	-2.6182	-0.5455	4.2955	0.7692	6.5417	0.0451	0.1661	-0.4591	-0.0822	-0.0069	0.1792	0.4959	-0.0814	-0.0509	0.2401	0.0045	-0.0484	0.2089	-0.041	0.1746	43.6829	40.1325	27.8408
7	2.8004	2.1181	1.7033	3.9132	0.014	3.1842	0.0244	-0.517	-1.2063	0.1654	0.2193	-0.1093	0.2172	-0.1689	-0.2709	0.2756	-0.0113	-0.0179	0.3103	0.1078	0.3179	19.3128	31.6412	21.7242
8	2.0154	-0.2045	1.8878	2.1461	-0.5986	3.0514	-0.0777	-0.1764	0.1759	0.1924	0.2401	0.598	-0.3449	-0.5603	-0.1184	0.2179	0.0324	0.0588	0.4546	0.1005	0.4212	3.8116	39.9285	17.287
9	1.4561	0.0697	0.0198	0.6327	-0.2265	0.6527	-0.0249	-0.0312	-0.0608	0.0108	0.0131	0.0237	0.0019	-0.0154	0.0142	0.1281	0.0014	-0.0254	0.1909	-0.0236	0.1741	31.5289	43.6111	1.2544
10	1.9713	-0.0443	0.3608	1.4922	0.5633	2.0022	-0.0125	-0.1413	-0.2841	0.0021	-0.0051	0.1162	0.0632	-0.0791	0.0193	0.1162	-0.0023	-0.0094	0.1811	0.0246	0.2093	24.4567	35.6377	8.3479
11	1.4258	0.0345	-0.1242	0.7363	-0.1664	0.8852	-0.043	0.1732	-0.0264	-0.0928	0.048	0.1356	0.0124	-0.1279	-0.0049	0.1558	-0.0116	-0.0477	0.2624	-0.0048	0.2483	17.9883	46.9809	-5.4047
12	7.4999	2.1433	7.6666	5.4864	3.9263	8.455	-0.6809	0.8737	-0.3011	-0.8536	0.8309	-0.4198	-0.66	1.9923	-0.1237	0.4665	-0.0386	0.1728	0.2474	-0.0213	0.2483	40.3889	63.8601	43.3927
13	0.6271	0.7722	-1.9548	9.6569	-0.4471	6.6299	-0.1515	-0.9685	-0.3185	-0.6068	0.8645	-0.4064	0.8249	-1.6473	-0.7223	0.1686	-0.0236	-0.0558	0.2214	-0.0161	0.2878	31.5903	36.4756	0.7372

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 200 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 201 through 273 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 274 through 345 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 346 through 371 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 372 through 398 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 10 through 31 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 32 through 64 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 65 through 215 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 216 through 298 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 299 through 393 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 2503 through 2503 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 503 through 503 )

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