PDB-6hto: Tryptophan lyase 'empty state'

ID or keywords:

Entry

Database: PDB / ID: 6hto

Title

Tryptophan lyase 'empty state'

Components

3-methyl-2-indolic acid synthase

Keywords

ANTIBIOTIC /

Radical SAM / NosL

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: 1.45 Å

Authors

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

Funding support

France, 3items

Organization	Grant number	Country
French National Research Agency	ANR-16-CE29-0019	France
French Infrastructure for Integrated Structural Biology	ANR-10-INSB-05-02	France
French Infrastructure for Integrated Structural Biology	ANR-10-LABX-49-01	France

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_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_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.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	6hto.cif.gz	346.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6hto.ent.gz	276 KB	Display	PDB format
PDBx/mmJSON format	6hto.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/ht/6hto ftp://data.pdbj.org/pub/pdb/validation_reports/ht/6hto	HTTPS FTP

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Related structure data

Related structure data	6htkC 6htmC 4r34S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4r34-2 6htk-2 4r33-2 4r33-1 6htm-2 7ajk-d 1xxv-d 2hnk-d 6htk-1 2fun-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: 3-methyl-2-indolic acid synthase

B: 3-methyl-2-indolic acid synthase

hetero molecules

91.5 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)	46.970, 92.610, 94.460
Angle α, β, γ (deg.)	90.00, 98.73, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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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 , 6 types, 1209 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-MET / METHIONINE / Methionine Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₁NO₂S
#4: Chemical	ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₃
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: Cl
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1189 / 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: 2.08 Å³/Da / Density % sol: 40.8 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 14-20% PEG 3350, 0.2 M KBr, 1 mM 5'- deoxyadenosine (5'-dA), mM L-methionine, and 15 mg/mL SaNosL (protein buffer: 50 mM Tris pH 8; 150 mM NaCl and 2 mM DTT)

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 10, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.45→47 Å / Num. obs: 257679 / % possible obs: 93.1 % / Redundancy: 5.29 % / R_sym value: 0.064 / Net I/σ(I): 15.25
Reflection shell	Resolution: 1.45→1.49 Å / Num. unique obs: 9677 / R_sym value: 0.767

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4R34

4r34

Resolution: 1.45→46.426 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.85 / Phase error: 21.01

	R_factor	Num. reflection	% reflection
R_free	0.1922	12577	4.88 %
R_work	0.1676	-	-
obs	0.1688	257679	92.34 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.45→46.426 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5871	0	99	1189	7159

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	6250
X-RAY DIFFRACTION	f_angle_d	1.261	8513
X-RAY DIFFRACTION	f_dihedral_angle_d	21.908	2340
X-RAY DIFFRACTION	f_chiral_restr	0.133	940
X-RAY DIFFRACTION	f_plane_restr	0.008	1120

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 (%)
1.45-1.4665	0.3402	414	0.3302	8252	X-RAY DIFFRACTION	92
1.4665-1.4838	0.2894	409	0.2845	7980	X-RAY DIFFRACTION	92
1.4838-1.5018	0.2803	419	0.2605	8053	X-RAY DIFFRACTION	91
1.5018-1.5209	0.2768	407	0.2618	8079	X-RAY DIFFRACTION	90
1.5209-1.5409	0.2918	377	0.2571	7309	X-RAY DIFFRACTION	84
1.5409-1.562	0.2766	419	0.2424	8138	X-RAY DIFFRACTION	91
1.562-1.5843	0.2456	433	0.2242	8183	X-RAY DIFFRACTION	94
1.5843-1.6079	0.2487	422	0.2254	8351	X-RAY DIFFRACTION	94
1.6079-1.6331	0.2404	420	0.2119	8255	X-RAY DIFFRACTION	93
1.6331-1.6598	0.245	428	0.2002	8262	X-RAY DIFFRACTION	94
1.6598-1.6885	0.2097	433	0.1886	8332	X-RAY DIFFRACTION	93
1.6885-1.7192	0.215	417	0.1842	8177	X-RAY DIFFRACTION	93
1.7192-1.7522	0.2166	420	0.1804	8174	X-RAY DIFFRACTION	93
1.7522-1.788	0.2171	414	0.1699	8153	X-RAY DIFFRACTION	91
1.788-1.8269	0.2002	377	0.1687	7395	X-RAY DIFFRACTION	84
1.8269-1.8694	0.1802	432	0.1656	8243	X-RAY DIFFRACTION	93
1.8694-1.9161	0.2097	432	0.1675	8409	X-RAY DIFFRACTION	95
1.9161-1.9679	0.1794	437	0.1552	8399	X-RAY DIFFRACTION	95
1.9679-2.0259	0.1747	433	0.15	8370	X-RAY DIFFRACTION	95
2.0259-2.0912	0.1923	428	0.1541	8350	X-RAY DIFFRACTION	95
2.0912-2.166	0.1798	421	0.1512	8406	X-RAY DIFFRACTION	94
2.166-2.2527	0.2088	414	0.1634	8136	X-RAY DIFFRACTION	92
2.2527-2.3552	0.2089	384	0.1653	7493	X-RAY DIFFRACTION	85
2.3552-2.4794	0.1984	442	0.165	8521	X-RAY DIFFRACTION	96
2.4794-2.6347	0.2033	441	0.1668	8521	X-RAY DIFFRACTION	97
2.6347-2.8381	0.1904	431	0.1653	8417	X-RAY DIFFRACTION	96
2.8381-3.1237	0.1922	414	0.1636	8299	X-RAY DIFFRACTION	93
3.1237-3.5755	0.1832	398	0.1507	7811	X-RAY DIFFRACTION	88
3.5755-4.5042	0.1337	429	0.134	8508	X-RAY DIFFRACTION	96
4.5042-46.4496	0.1585	432	0.1542	8126	X-RAY DIFFRACTION	92

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	1.3302	0.0438	-0.8311	1.1729	0.4297	3.3196	0.0816	-0.2172	-0.2257	0.3451	-0.0642	-0.0651	0.3837	-0.1328	-0.0157	0.2489	-0.0683	-0.0016	0.1674	0.0398	0.2156	-8.633	-33.3037	-29.2933
2	0.7626	0.1267	-0.1732	0.5672	0.0905	0.9752	0.0038	0.074	0.0243	0.0017	-0.0007	-0.0024	0.0276	0.0317	-0.0037	0.0861	0.0087	-0.0017	0.0902	0.0043	0.0999	3.5394	-15.0236	-52.4025
3	1.5596	-0.3535	0.0056	1.9032	-0.084	1.9195	0.0083	0.0074	-0.1291	0.0394	0.0039	0.1191	0.1194	-0.175	-0.0049	0.0936	-0.0284	0.0035	0.0845	-0.0067	0.1107	-8.6329	-25.6888	-47.9759
4	0.7305	0.2759	-0.0568	0.9071	-0.0362	0.9195	0.0377	-0.0655	0.0691	0.0928	-0.051	0.0472	-0.0689	-0.0724	0.0085	0.1066	0.006	0.0074	0.1148	-0.0121	0.1111	-2.7327	-11.2541	-39.6995
5	4.6751	-0.9729	1.0087	4.4002	0.1046	3.6848	0.0556	-0.2559	0.3036	0.2556	0.0026	-0.2801	-0.2551	0.313	-0.0085	0.137	-0.0448	-0.0067	0.1383	-0.0105	0.1183	13.6928	-6.9034	-35.6581
6	7.2532	0.0628	-3.8597	7.2489	0.6926	6.5212	-0.0818	-0.0729	0.0061	0.2935	-0.0698	-0.0609	0.1475	0.0772	0.0845	0.0523	0.0127	0.0008	0.0974	0.0297	0.1142	-5.4014	-15.6049	-53.1285
7	1.9105	-0.4056	0.3731	2.094	0.4748	4.2696	-0.0509	0.1893	0.1924	-0.0991	-0.0067	-0.1305	-0.4675	0.0078	0.0428	0.2427	0.0207	-0.0209	0.1446	0.031	0.1699	2.0639	3.1538	-107.9573
8	0.5219	-0.1477	0.0266	0.559	-0.2083	1.8329	-0.0044	-0.0488	0.0064	-0.0246	0.0141	-0.0075	-0.011	0.0287	-0.0073	0.1076	-0.0227	-0.0035	0.1178	0.0037	0.0969	7.6092	-14.7211	-81.7532
9	2.2573	-0.0786	0.3632	1.3824	-0.3195	2.4886	0.0013	-0.0093	0.1784	-0.0621	0.0026	0.1424	-0.1587	-0.2303	0.0791	0.1268	0.0037	0.0076	0.1046	-0.003	0.0688	-1.3413	-6.76	-87.7102
10	1.0648	-0.0286	-0.2518	1.2872	-0.326	2.3031	-0.0321	0.002	0.074	-0.0281	0.0366	0.0389	-0.2685	-0.1993	0.0078	0.1526	0.023	-0.0211	0.1156	0.0055	0.1151	-1.0566	-3.0963	-89.4889
11	0.8241	-0.0306	-0.0263	1.2896	-0.7379	2.1623	0.0073	0.0443	-0.0384	-0.1222	-0.0435	0.0575	0.1642	-0.0632	0.0489	0.172	-0.0224	-0.0103	0.1438	-0.0114	0.1101	5.8251	-14.3123	-99.014
12	2.7047	-0.3571	-0.8904	1.9529	-0.1348	2.9832	0.0116	0.2126	-0.2437	-0.2056	-0.0366	-0.0572	0.3912	0.1758	0.0474	0.2066	0.0277	-0.0155	0.1501	-0.0048	0.1039	14.485	-25.6052	-90.9189
13	6.1626	-0.2489	4.4949	4.4982	-2.2775	5.7688	0.2351	-0.1092	-0.0868	-1.1922	-0.3753	0.2336	-0.6613	-0.2507	0.1143	0.1473	-0.0079	-0.0193	0.1277	0.0118	0.0933	-0.783	-14.2104	-83.9486

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 14 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 371 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 372 through 394 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 502 through 502 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 15 through 64 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 65 through 190 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 191 through 215 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 216 through 273 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 274 through 345 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 346 through 393 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 502 through 502 )

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